If you use 2.6, the last free version of No$GBA, you have to manually set the NDS backup media for every game you play. To know what to use, click on the link in my sig, use the dupe search to find the game's scene release page and divide the numerical value of the savetype by 8 (so Advanscene's EEPROM 512kbit translates to EEPROM 64k in No$). Also, multiply the values of Flash savetypes with 1024 before doing the above step.
As for renaming no$gba.ini to firmware.bin, sorry but :hdbash:
Apart from being used by the same program, they have literally nothing in common. On the upside, you no longer need firmware to play commercial games and a new no$gba.ini file is automatically created with the standard settings if you delete it, next time No$ is closed.