The scripting runtime of CS6 point apps is using flex sdk 4.5, CS5 and CS5.5 were using 3.4 - therfore you will need to set them up as seperate projetcs. You can still package and distribute them as ZXP Bundle. Check out the ZXP Bundle tab in Build Manifest Editor.
This will be a big problem, keeping 3 different projects is really difficult as they are very large ones.
I had the sincere hope that the new updates would make it easier , at least with an easy "compile for ... " feature
Making the CSAW libs 4.5 only was a huge mistake in my book! (I can't believe I missed that in prerelease.)
That's a giant step backwards, and I'm not going to be using CS6 CSAW libs anytime in the near future. Backwards compatibility is way too important, and multiple projects is a horrible way to work...
Just another reason to stick with ExtendScript...