Guide tracks and ideas into Cubase SX, a little bit of editing and cutting to organise a basic arrangement, then re-record all backing tracks properly. Drop in the leads, harmonies and counter melodies (dedicated track each). Midi channels for drum tracks and other plug-ins.
When I'm happy with the recordings, then export each track as a wav file and import them into ProTools for mastering and cleaning up.
Cubase is excellent for recording but ProTools kicks ass when it comes to mastering the final product.