Absolutely you can still use the pedals into the TD-6 trigger inputs while using the MIDI In for the Zendrum.
I would highly recommend doing that first to make the transition easier.
That's what I did too, until I realized after a couple of gigs that I could play 32nd note bass drum fills with my hands in the middle of Mustang Sally and make my bass player run screaming off the stage...(what fun!!!)
Mainly I would say do ANYTHING that makes you comfortable and have a good time. There are no rules here, only imagination and experimentation. Go for it.