Okay I got it figured out. In order to get the save files to work in VBAlink I had to convert it using this website
http://www.shunyweb.info/convert.php I selected the EZflash iV as the input and No$GBA as the output file. I used the the VBAlink version 1.8 and I could not get the trading to work I kept getting the connection error. I had to use the 1.7 edition to get it to work.
Okay so here are the steps
-first you have to download the .roms you need and the VBAlink 1.7
-next you need to convert the saves you are using
-now start two VBAlink windows and use the rom you want
-import the .sav that you converted
-when you start the game it will say that the save file is corrupt and it will load previous state and it loads your good save file
-in both games go to the pokemon center and when you go to trade you need to make sure that the pause when inactive is not selected
-speak to the lady and you will start into the trading area
-you have to make sure that the pokemon you want to trade are in the same location in your six because you have to move both windows at the same time or the link will break
-after you trade you can in game save and two saves will be created .sa1 and .sa2 they are located in the save location as the .roms I am pretty sure that .sa1 is the one you want put it back on the EZflash and change it to .sav
-when you load the game the same message will appear save file corrupt but the game should load fine and when you save in the game again a new save will overwrite the old one and it will be good to go.
I hope that is understandable lol.
Two problems
1 it is not perfect it takes several tries to get it to work and when you are trying to enter the save room you have to have a certain window selected not sure which one
2 I have only tried this with leaf green and fire red it would not work with fire red every time i loaded the save back on to the EZflash it said save file has been deleted not sure why
leaf green works perfect
if anyone else tries this with other games or figures out how to make fire red work let me know.
hope this helps