The mainland tours are generally all day affairs (ending up with copious amounts of demon rum being served to the unsuspecting)because of the distance involved.
Not familiar with Bottom Time. We've used Amigos Del Mar, Fantasea (Victoria House) and the Blue Hole Dive Center. We used the Blue Hole group the last three times and the diver (SWMBO) was pleased. All the dive operations will pick you up at the dock nearest your lodgings, so pick the one that sounds right.