Okay I figured it out. But this is a little different.
Open game in VBA and load your save file.
File ----> Open Rom
File ----> Load Game or F1
Then go to Options ---> Emulator-----> Save Type-----> Make sure it's on Flash 128k
Then save it like on a regular GBA in the game. Start----> Save-----> Yes. Done
Go to File------> Export----> Battery. Now just save it. Now go to where it's saved. It should be the one with .SAV in capital letters. Now you want to rename it. For example------> My Pokemon saved battery is called NaranjaEnglishB2.SAV (A hack called Pokemon Orange, but the name is in Spanish). So you would rename it like this NaranjaEnglishB2.sa1. Doesn't matter if it's capitalized or not.
Now open VBA Link-----> File-----> Open-----> NaranjaEnglishB2.rom
Then go to File---------> Import--------> Battery-----> NaranjaEnglishB2.sa1
Importing a Snapshot file will erase any saved games and reset the emulator. Do you want to continue?------------> Yes
Then wait for it to get to the Continue/Start New Game/Options Screen. And there should be a continue. Click Continue and now you can save.
Shift F1.
If you followed it like that you should have no problem. If you have any questions message me or reply. Peace from the East.
Also if this doesn't work for you then it might be because it's the latest from the vba link website. The one with with both wifi/lan, cause that's how I had to do it for it to work.
Now if only I can get the stupid linking system to work. I can never trade. It keeps going to errors. Screw it I'll just go back to regular VBA.