Hi, I'm trying to get Mega man star force Leo to work, and I got it to work on the no$gba, problem is I can't make it bigger then the normal set up, which hurts my eyes. Also I have like no idea what I am doing to save this emulator, is there any emulators that work life the VBA or something that I can make battery files or no?

You'll just have to deal with the size. You have to configure the emulator correctly. Plenty of answers can be found here.
http://forums.ngemu.com/no-gba-discussion/

With the size problem, right click NO$GBA.EXE, press Properties. Go to Compatibility tab. Select "Run this program at a resolution of 640x480". Press OK.

Now NO$GBA will start at low resolution (which means that it will show bigger). Don't worry, the effect ends when you close NO$GBA. With the save type, for MMSF it's Flash 512kb, if I remember correctly.

Thank you for the size help, I can now see the game just fine. I tried your tip on the save file and now it will save the game just fine, but I want to know how to make separate battery files for one ROM, cause me and my bro share this pc. Also How do I set it up where the section game it loaded up get that separate battery file?

Just make a copy of the NDS file, and put it someother name. Example: MMSF Leo [your name].nds, and its copy, MMSF Leo [your bro's name].nds. Then NO$GBA will create differents battery files for those roms.