Dont plan!, wake up, have breakfast, pick a spot, drive there, go diving. If a spot is crowded or does not look ok to dive (for some reason of other circumstances) then pick another, drive there and go diving ;-)
My sentiments, too. On my first trip, I did all this "research" online, asking people what the "can't miss" sites are. After two days on Bonaire, I realized how silly that was. In time, you'll cover most of the ones you hear people mention, regardless of what order you do them in. There's no right or wrong way to pick sites--whatever works for you. For one's first visit, don't feel compelled to strategize over what sites to visit in what order, etc. Open the BSDME book, and for your morning dives pick a site or two that sound good, perhaps somewhere to the north of where you are staying. Then pack up the truck, get tanks, and go. The exception might be the far north--where the road becomes one-way and you have to commit to going around the whole loop, which will eat up much of your day. When you want to explore the northern sites, plan to make a day of it. As others have pointed out, if you arrive at a site and the waves look a little rough, then drive somewhere else. No big deal. Return for lunch. In the afternoon, pick a site closer to where you're staying, or to the south of where you dived in the morning. As you've read, the far southern sites can be more challenging--I didn't do any of them on my first trip, since the dive shop said the conditions were a little rough. In any case, you probably don't want to be driving all over the island in one day. We tend to pick our sites based on whether we feel like going north, south, or staying close to town. Even the sites close to downtown Kralendijk, like Yellow Sub, are perfectly great. Sometimes we just decide on a direction, knowing there are several sites in that region that would suit us, drive off that way, and then make an impromptu decision on the particular site. After two days on Bonaire, you will have a good feel for where (and how far) you want to go. Some days, we decide at breakfast that we just don't feel like driving all over the place. Other days, we decide we're up for an adventure.