As Gaz said, I believe all the shops will set you up for whatever trip you desire. However, please note that the shop you with which you are doing your regular dives may not actually do the trip itself. They may send you with another shop. But, yes, as Gaz said, let the shop know right away that you want to do a certain trip. For example, Ecologic does offer a trip up to the northern part of Ambergris (Basil Jones area) but they need a minimum of four to do it. So, three of us put our names on the list. We'll see what happens.
Also, I would not be concerned about packages. In fact, I wouldn't even book your diving in advance unless you feel personally comfortable with the shop. Last year, I decided to use Chuck and Robbie's in advance and it worked out well. This year, I e-mailed a few shops but waited until I arrived to meet with Ecologic and was pleased with what I saw. Dive shops are not "one size fits all" (at least from my perspective). So far Ecologic has worked out well for me. As far as packages, again they are fine if you know the shop and want to commit. But what if you change your mind? What if the weather doesn't cooperate? Your shop may not give a refund for unusued dives. I'd rather pay a few more dollars per dive to be able to have some flexibility to make changes. Yes, there is always a chance that the shop you want to dive with may be full at the time you want to go. But, from what I have seen thus far during this trip and from my trip last year, things work out.