I have figured it out, i just got past the infinate time warp scene so this works. On the EZFlash V you need to make a folder called "CHT" all caps and put the ezarcode file in there (http://cheats.gbatemp.net/). Then you need to boot up the card and make sure that the icon with two arrows in blue. Next select the chrono trigger rom and it will give you a list of cheats. activate the first game fix cheat by pressing right and not the second, and any other codes you want to use. next press 'a' to start the game. once you are in the game press 'L'+'R'+'START' at the same time to activate the codes, and 'L'+'R'+'SELECT' to turn them off after.
happy time travels!
happy time travels!