You'll probably want to update from JKSV to
Checkpoint. As for the rest, follow the instructions carefully. As it says, open the game you want to copy your save from. Then reboot into GM9 with Luma's chainloader (power off while in-game, hold Start while turning the system on). Use GM9 to navigate to SYSNAND VIRTUAL (S: Drive) and in there should be your save file (gbavc.sav) as mentioned. Copy it to a new folder on your SD card (0: Drive). Wash, rinse and repeat for every game you want to back your saves up from.
It's also important to note here that the .BIN files Checkpoint and JKSV dump are completely different from GBA saves. AFAIK, Checkpoint/JKSV isn't compatible with GBA titles on the 3DS family. In other words, unless there's something funky going on with your game, you're looking for a .SAV file, not a .BIN.