Well, you can use either one. There are limitations to using either mode.
For Clean Mode, it limits the things that you can use, which means that you cannot bring up the In-Game Menu while you're in a game. Even though that limits you from using RTS, RTC, and RTG, there is a possibility for Clean Mode to decrease the chances of freezing in a "new, released" game. I don't use Clean Mode that often, because it is unnecessary for the old games that I play. I guess you would interpret it as using Clean Mode as a chance to bypass AP in new games.
As for Patched Mode, it's basically the opposite of Clean Mode. You have no limitations when you use Patched Mode, which means you can use the In-Game Menu while in a game, but the chance to bypass AP for new games while in Patched Mode is almost non-existent (I wouldn't say fully non-existent because most of the new games that I've tried so far in Patched Mode works).
That's pretty much the difference between the two modes.