My wife and I did this a couple of years ago. What we did was grabbed a taxi (and opted for one that was a van, so that we'd be comfortable and were up in the air to see better). We negotiated a price, which (if memory serves me right) was $70 for four or five hours (I gave the driver $100 at the end, as she was very good, and very patient). Our primary reason for the taxi was so that we could enjoy ourselves along the way, and be pure tourists, as well as being able to partake at a few of the beach clubs, without worrying about getting pulled over.
As was mentioned above, we are also "clockwise" people, so we headed east on the cross-island road. Our first stop was the Mayan ruin,
San Gervasio, where we got a guide who took us through the site. Next, we stopped at some of the places we had frequented previously, such as the bar right at the end of the cross-island road called
Mezcalitos. We then hit a couple more of the beach clubs along the way south, having lunch at one of them, and finally stopping at
Rastas. Whenever we stopped, we made sure to bring our driver a bottle of water or soda pop.
We then went into the Punta Sur park, but didn't do everything that was offered, as we had to watch the clock, we could have budgeted our time and stayed there longer, though, and cut out a few of the beach clubs. I have to admit, we've only been to El Cedral a couple of times, and then very briefly, so can't make a recommendation there, and we did not stop during this trip, either.
Regardless of how you do it, I hope you enjoy yourselves!