Here's how I do it. I first record a rough version of the guitar part to the metronome in Cubase. I then export this as a wav.-file, which I import into Fruity Loops. Now I can start creating the drums (making sure the bpm is set correctly) to the guitar part.
I then export the whole drumpart again, and import it back to Cubase. When I'm done recording and I want to lets say bring up the kick, I just return to FL, adjust the drums, and export the drumpart as the same wav. again, so the it gets 'updated' automatically in Cubase.
This way the drums only take up one track in Cubase..