Get to the pier and get your required "checkout" dive out of the way as soon as you get there - otherwise you might lose some dive time on the first full day. Once you have your dive locker/key and weights, you're basically on your own from then on out. Reason I say this is that if you miss that first day, then you can't (last I checked) sign up for the next AM's boat dives. I've never done the boat dive package (just a la carte) but last time we were there another couple was getting upset that they might have trouble fitting all of their boat dives into the week because of something like this. (I could be wrong...).
Overall it's a smooth running operation. They know why you're there (to dive) and have planned for it. The dive shop crew is always very helpful. Allocate some tip $$ to them, they're worth it). Listen and ask questions. They were quick to help us out when we had a minor equipment problem once with some emergency zip-ties.
Get a copy of Bonaire Shore Diving Made Easy - it's cheat-sheets for all of the shore dive sites.
Take advantage of the house reef and do some easy sunrise/sunset dives (aquatic shift change...).
Swap tanks out when you get back from the last dive of the day, if you're planning on doing early drive-and-dives. They're safe in the truck in Buddy's parking lot overnight.
Get your Nitrox cert and use it while you're there (if you don't have it already).