Unless they have finally joined the two together...there are two operating terminals.
Take the Express bus....you will be glad you did. One leaves from one station at 10 or 10:30..and from the other station around 11am. The cab drivers know which is which.
Once in San Ignacio....any of the cabs can take you to the resorts....most are not far from Town. Clarissa Falls is about a 10 minute ride out of town...nice place.
I wasn't real impressed with the food there....but I hadn't had a chocolate shake in over a year...and it was damn good...LOL
The grounds are beautiful..and the falls are nice. Be sure and take a pair of water shoes though...the bottom is nothing but rocks and painful to walk on barefoot.