Fair enough. I tend to avoid the all in one emulators (seldom as good as standalone, lots of drama). Might also want to note what you are aiming for in the future.
In that case the main things to look for are extra headers, extra footers, whether they need a special name and possibly compression.
Headers and footers are little extra segments that go at the start and end of a file respectively. Some emulators and flash carts will add these (and can also go for ROMs as well) to note what game it came from and some other stuff too if the original save did not feature such things (generally speaking if the save lives on a cartridge or maybe a floppy disc then it will not note what it goes with -- it is not like the original game is going to be saving here, there and everywhere. Anything where the console itself has profiles to log in with, or save management on the menu will have data to match a save back to the ROM it came from). What this header or footer might contain will vary between things, and sometimes it is not necessary (or if the emulator/save editor/flash cart/original cart you are going to does not need/expect one then you might have to chop it off)
Special name will tend to be say naming a save for the game's internal serial and version so you know what it goes back to.
Compression is just that. Sometimes if you have say 512K saves for each game despite most of them only being 64K or less (happened for most DS flash carts, adds up to quite a bit as well if you have a few dozen ROMs) then compression can save some space. What does what varies here, though for PC most of the time it is something that 7zip or something can handle rather than all custom. You might also have an option somewhere in the emulator to disable save compression.