Diving with Bas and diving with ECD are each unique. Bas (who is indeed worth it) will take to you a site he likes for the day (and your skills), and train you how to enter and how to exit. (As to the importance of this, read Richard's Cai thread.) Bas took my wife and me, after confirming that she did not wear nail polish, to Boka Spelonk; there was considerable current going opposite the usual direction, but Bas is one with the sea and the dive was challenging but terrific.
But the OP asked about boat dives, which of course is, on the east coast, ECD. They use a purpose-built boat, and the dives are basically drift, with a healthy amount of finning. The trips are two tanks; the first is a reef shoulder similar to the west side but scaled up and with some different animals. The second tank is a whole different thing; first, a shallow sandy bottom with everything from sea horses to nurse sharks (and, once when we were there last year, 13 eagle rays together), and then a laugh-through-your reg extravaganza of turtles. We've been in some pretty good chop and swells other there.
As to boat dives generally, I don't think packages, although widely available, need be arranged in advance unless you want to work with a particular resort or an operator like Dive Friends. We have settled on two operators; Div'Ocean, (divoceacnbonaire.com) is a two-man operation; they run a quick outboard with max six divers (usually fewer, and sometimes two), and go to the north sites, all around Klein (including less-traveled sites like Southwest Corner and Forest, when conditions allow), and the southern sites. Ebby Jules (divewithebby.com) has an even faster outboard and is a lot of fun to dive with; he'll go wherever you want if conditions allow.
Lots of folks look askance at boat divers, but we're oldish, my buddy's got a good bit of titanium, and I haul a camera along. We usually do about 2/3 shore dives, three or four of which are at night, and 1/3 boat dives, and we choose boats whose captains don't mind if we're a little late to the dock. That's what I call "dive freedom."