I don't use Action Replay for the game, ruins the whole purpose. Some other games it may be fun to use Action Replay on and doesn't really ruin it, or you only do it when the game is finished, but the way I see it, unless you have already completed the game 100%, you shouldn't be using an Action Replay on it at all. I have Action Replay DSi and have never once used it for Phantom Hourglass because I think that all of what I've said is true.
I don't advise using Action Replay on your main playthrough of the game. Cheating right away generally takes the fun out of the game for players such as myself and others around here that I know of.