If it's not 512 kb, use Shuny's Converter to convert it to a R4 (512kb) save. Then rename it to the exact name of the rom, except instead of ".nds" it should be ".sav" Like Destructobot said above.
And you can put the save file wherever you want on your SD, but I like to put mine in a games folder where all my other save files and games are stored.