Audyssey 'should' do the same as the EQ. But if you really want to dial things in then REW is awesome (I even purchased a mic just for this purpose :)).
I guess the choice for your fronts is really up to weather you plan to listen without a sub. I went with towers since I often listen to...
I suggest starting with matching speakers up front. Since your center is the best of the 3, matching the other 2 should be done first. Looking at Polk's site it looks like the S55 and S60 would work (or the S15 if you want a small bookshelf).
For the sub, I assume you calibrated everything...