It depends on whose training schema you're using. If you want to work with Andy Coggan's training levels then you'll base everything on FTP. If you go with Ric Stern's zones you'll base things on MAP. I'm sure there are other systems out there that use other reference points. If you haven't done so, you should read Training and Racing with a Power Meter or surf over to Ric's site and have a look at his approach:
http://www.cyclecoach.com/
If you work with WKO+ you have a couple of options regarding your training levels. I use Coggan's levels and like his system but like Ric's approach as well. Anyway there are a lot of ways to skin this cat so you need to pick a system and follow it.
Good luck,
Dave