I would connect to the existing ducts if possible. If your original a/c goes out at least you can have cool air flowing to your entire unit.
On my Columbus 365RL I have one thermostat for both A/C uits (Zone 1 & Zone 2)
Not sure if true but my dealer told me that if I was adding a 2nd air to my unit it could not be ducted. The only way to have it ducted was to order from the factory. So that's what we did as the wife and I wanted it ducted.