I made the day trip, obviously an overnight would have been better but I too didn't have the option. It was an amazing experience, I'd highly recommend it.

Holiday Hotel booked our trip through Tropic Air, we flew to Flores (with a stop in BC) and were met there by a guide who drove us to the site. Of course you can't see all there is to see in a day, but you do have plenty of time to wander around and take in some of the highlights.