Turn your DS off and on quickly, then go to the saver tab and choose your FF V save file, press A to save the data in the supercard RAM to the save file in the sd card.

 

It sounds like you upgraded to the new SC firmware, which doesn't let you do a QPC save: quickly turning your DS off/on etc. For FF V to run at a decent clip on a Supercard you need to disable "restart" in the SC patcher; but then how do you save?

Here's one solution that others have helped me with. Only enable the "saver" patch in the FF V rom, and then run the resulting rom through the "fastrestart" program. When you want to save, do an in-game save, an L+R+Select+Start to reboot to your SC menu, and then navigate to the "saver" menu, select your FF V's .sav file, writing it to your flash card.