I stayed and dived with Buddy Dive about a month ago and it was great. You will love Bonaire it is an excellent place to increase your diving skills and seeing some great marine life. The reefs are healthy and have plenty of fish (for the Caribbean), including some of the rarer little stuff, such as frogfish and seahorses.
Buddy's house reef has a resident tarpon called Charlie, and he will come seriously close on night dives. It is only 3m deep or so where he hangs out, so have fun!
As others have said, the most-important thing to do is get some hard-soled booties. The coral will shred the soles of lesser booties (I know!) and, as some of the sites can be a bit rough getting in, you will find it a lot easier. Also, watch out for the black sea urchins they tend to live in cracks in the shallows, so if you have to put your hands down to steady yourself, make sure it is on a piece of dead coral or rock and not something spiky!
Completely off diving, you have to eat at Casablanca's at least once the mixed grill for two is large enough to feed four!!!! Damn good value for money!
Mark