I'm a bit clueless how to patch these...should I use the arp in the main patch and route the midi through the internal midi port?
i am a bit clueless as well. isn't part of the fun of arpeggiators that they are monophonic? (but by changing notes rapidly you get the impression of polyphony)
I'd do it in the main patch and use internal midi.
I think having it inside the poly patch would mean each note would have it's own arp which could confuse things when you're holding a chord or whatever
They are also nice with poly synths because you can smear the notes nicely into each other with long release.
did you plan to write your own arpeggiator? or use cpwitzes? if you need poly i would also use internal midi