“I’ll also have to research Media Manager in FCP 6 as I was always wary of FCP 5 Media “Mangler” issues.”
Llewelyn’s advice is excellent. Workflow is everything. As for Media Manager, I’ve been using it ever since it was first introduced and have personally *never* had any problems. Most problems are user error. You can certainly mangle things if you tell it to do all the wrong things. Just take your time and carefully check all your settings. If you have the space, use “copy” instead of deleting the original media. Also, pay attention to things like Nests and Speed FX. I’d take everything out of nests before MM’ing and pre-bake your speed fx.
HTH