MIDI to style, same way that several others do it. You either make different SMF's, one for each section, or you make one MIDI file with Markers for each section (the Korg way).

Intros and endings are no different really from making a normal tune in a sequencer (other than different ones for major and minor).

It's not really a bad system IF you are already familiar with a computer sequencer... Main problem is you don't really get to hear the style in context (how well the fills transition, etc.) until you import into the arranger. I imagine a lot of back-and-forthing would be necessary before it comes out the way you want it. Mind you, just making them inside the box involves a fair bit of that!