You can always pre-patch the games beforehand with GABSharky or use a trainer.
Follow the links below, download the Stevens Cheating Guide, and you should be fine.
Post with link to Stevens Cheating Guide
Guide to Using GABSharky
More General Code Converting Guide
You can also look into trainers for various games, and GBAATM, which I believe allows you to make your own trainers.
Other than patching, though, there is no way to use cheats on the 3-in-1 on anything besides the EZ-Flash V, and even then I'm not too sure on how it works.