Ok I just tried it an it's fairly straightforward.
Pressing A overwrites the current .sav file on the SD card that you are highlighting. It doesn't matter if the name of the save isn't the same as the game, it will still overwrite it.
Pressing B will create a new save file based on the metadata for the current rom and name it correctly.
So for each game you will want to press B.
In fact the first time you use it you cannot press A because there are no existing save files on your SD card to overwrite.
I haven't tested the saves it produces but I'm assuming they are okay.
The program also contains an EEPROM backup utility and it says something about that being different which I haven't really bothered to try and understand as I've only backed up the battery backed SRAM saves so far.