Acabo de dar con la solucion!!!
Hay que abrir el M3 Game manager y hacer doble click sobre un backup, entonces se te lanza el M3 Save Manager. Aqui esta toda la info. En negrita lo interesante (al parecer para que te lo guarde en el save especifico hay que pulsar el boton select depues de haber arrancado el M3)
Saver Manager:
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The Save Manager window of "M3 Game Manager" will appear after double-clicking a GBA or a NDS game form the game list of "M3 Game Manager".
The function of Buttons:
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Button: Read (Save data into PC)
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Function: Read in the data from "M3 saver file" and store it into PC.
Operate: Select one of the saver files from the list. Click the "Read" button. The data of the selected file will be copied into a new file and the file can be stored into any directory of your PC.
Button: Write (Copy data into CF/SD)
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Function: Write game save data into the "Saver File" of M3 adapter.
Operate: Select one of the saver files you wish to write data into. Click the "Write" button. A window will appear and ask you to select the source file. The data of that source file will be overwritten into the selected saver file of the M3 adapter.
Button: Create Saver (Copy and create saver file)
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Function: Copy and create one more backup saver file within the M3 adapter. It can be used to store one more game save data.
Operate: Select one of the saver files from the list. Click the "Create Saver" button. A window will appear and ask you to input the name of the new created file. A new saver file will be created then and it will appear on the saver list.
Button: Create bank (Create bank saver file)
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Function: Create one more bank backup saver file within the M3 adapter. It can be used to store one more game save data.
Operate: Select one of the saver files from the list. Click the "Create bank" button. A window will appear and ask you to input the name of the new created file. A new saver file will be created then and it will appear on the saver list.
Button: Delete
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Function: Delete the saver file from M3 adapter
Operate: Select one of the saver files from the list. Click the "Delete" button. The selected saver file will be deleted. The deleted file will be disappeared from the list then.
Button: Rename
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Function: Rename the saver file for easily memorize
Operate: Select one of the saver files from the list. Click the "Rename" button. A window will appear and ask you to input the name of the saver file you wish to name it.
eg. a game called "Nicegame.nds", you may rename it as "Nicegame-level 3".
Button: Read .sav (optional)
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Function: Only read the portion of normal game save data within the "M3 saver file" in and store the data into PC.
Operate: Select one of the saver files from the list. Click the "Read .sav" button. The normal game save data of the selected file will be copied into a new file and can be stored into any directory of your PC.
(We recommended that users use the "Read" button function to backup the game save data for M3. (.dat file) However, "Read .sav" function is good for backward compatible for another flash card saver file format.)
Button: Write .sav (optional)
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Function: Write the game save data of .sav format into the "Saver File" of M3 adapter.
Operate: Select one of the saver files you wish to write data into. Click the "Write .sav" button. A window will appear and ask you to select the source file. The data of that .sav source file will be overwritten into the saver file of the M3 adapter.
(We recommended that users use the "Write" button to write .dat file data into M3. However, "Write .sav" function is good for backward compatible for another flash card saver file format.)
Tips:
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You may copy games by using the "M3 Game Manager" or without using the "M3 Game Manager". The games are also able to run in consoles properly. However, the procedures of copying games via "M3 Game Manager" will automatic create the default saver files for each games. This default saver is used to carry the game save data and the M3 Save Management System will automatic copy the up-to-data game save data into that default savers file. Thus, the game save data for each game can be continuously to keep it up-to-date.
Applications:
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Simple step of copying game and storing game save data into CF/SD:
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By clicking the "Write" button from the main interface of "M3 Game Manager". A window will appear and ask you to select a game in which you wish to copy into CF/SD. After selecting a game and confirming the process by clicking the "OK" button. The game will be copied into CF/SD and the default saver file corresponding to that game will also be created within CF/SD. Put CF/SD into M3 and play with it in a console. After playing a game, the game save data is temporary stored into the SRAM within the M3 adapter. Rebooting the console, the game save data will be automatically stored into "Default Saver". The game save data will continuously be kept and it will restore back to SRAM after you select loading that game every time. (The file name of "Default Saver" = "GAMENAME.dat" in which storing into NDSSAVE directory for NDS saver, GAMSAVE directory for GBA saver. eg. the default saver file name of a game NICEGAME.gba will be "NICEGAME.dat".)
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Step of storing more than one game save data for a game:
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After copying a game or double clicking a game in which have been existed in the CF/SD, the Saver Manager window will appear on the screen. Select one of the saver files from the saver list. Click the "Create Saver" button or the "Create Bank" button. A window will appear and ask you to input the name of the new created file. Input a saver name and click the save button. A new saver file will be created. Put CF/SD into M3 and play with it in a console. After playing a game, the game save data will be temporary stored into the SRAM within the M3 adapter. Rebooting the console, the game save data will be automatically stored into "Default Saver". Press the "Select" button after entering into the "GAME" icon. The "GameSave Backup" menu will appear, use <- -> to select a saver file in which you wish to store the game save data into. The current game save data storing in the SRAM will be copied into the selected file. After exiting the "GameSave Backup" menu and selecting a game to load, you may use <- -> to select any game save files corresponding to that game in which you had stored into CF/SD before. Once you select the saver file, the data of the selected saver file will be copied into "Default Saver" and the games with the selected game saver data will be loaded into consoles and SRAM.
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Step of storing game save data into PC:
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After playing a game, the game save data will be temporary stored into the SRAM within the M3 adapter. Rebooting the console, the game save data will be automatically stored into "Default Saver". Power off the console and connect that CF/SD into the PC. Run "M3 Game Manager", browse the game storing in CF/SD from the main interface of "M3 Game Manager", the Saver Manager window will appear on the screen after double-clicking the game. The saver manager window will appear and all of the game save data for that game will be listed out. Select one of the saver files you wish to retrieve the data. The selected game save data will then be copied into PC after clicking the "Read" button.
IMPORTANCE: To keep the game save data up-to-date, it is necessary to reboot the console after playing a game. As the last game save data is only stored into the SRAM of M3 adapter during game.(Not yet storing into default saver file). The game save data will be automatically stored into default saver file after rebooting the console.
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Step of restoring game save data back to M3 adapter:
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Browse a game storing in CF/SD from the main interface of "M3 Game Manager", the Saver Manager window will appear on the screen after double-clicking one of the GBA/DNS game. And all of the game save data storing into CF/SD for that game will appear at the saver list. Select one of the saver files you wish to write data into from the saver list. After clicking the "Write" button, a window will appear and ask you to select a source game save data file. The data of that source game save data file will be overwritten into game save file within the M3 adapter after confirming by clicking the "open" button.
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Reduce the size of .dat file for GBA Normal game:
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Now, users may place a .dat file of size 129KB to store normal GBA save data. The .dat file of size 1MB support storing both "Instant save data" and "Normal game save data". The .dat file of size 129KB support storing only "Normal game save data". The bank 129KB .dat file can get from "M3 GAME Manager" installation directory (....\GAMESAVE\bank.dat). To make use of this .dat file, please put the "bank.dat" file into the "GAMESAVE" directory under the root directory of CF/SD card. In addition, users may change the name of the .dat file for easily file management or create more .dat files to store more game save data.
Lo unico que no entiendo es la diferencia entre crear bank o saver (en la descripcion pone lo mismo) y que segun pone el M3 SIEMPRE guarda en el save por defecto, independientemente de que hayas cargado la partida desde oro save, luego debes ser tu mismo quien te encargues de copiar ese save guardado en el default al save que quieras. Viendo esto supongo que si quiero tener dos partidas de nintendogs necesito 3 .dat distintos, uno que sea el default (el que genera el M3 manager y que siempre se va a sobreescribir) y los otros dos, uno para mi y otro para mi primo
En cuanto pueda lo pruebo a ver...
PD: Perdon por el tocho pero creo que es algo muy interesante