Here's what we did.
Piled all our gear loosely in the bed/backseat - everything needed for 2-3 dives (no bags/cases) the only exception was a spare video battery which I left between the seats - and water.
Bonaire is a pretty small island so you are never more than about 29 mins from where you're staying.
Also a Dive Friens tank exchange if you are using them - they have about 6.
Just 2 of us so we carried 4-6 tanks all week. Get a few tank orings also - saves a drive.
I really would not bother with alternating dives or leaving a sentinel.
Throw the spare tanks in the back, they won't be touched,, All are marked and won't be filled by another shop so have no value.
Make sure to have some sort of small waterproof case for small items like glasses etc. I bought several pairs of sunglasses at the dollar store that would be no loss if taken, all came home with me,
So did the ratty tshirt I wore between dives. I stay in my dive boots all day.
After a few days we evolved a routine - our condo at BelMar was on the main road a few mins. south of town. So we would dive 1-2 dives either north or south then drive by, do any needed exchanges and dive the other area. Several options for lunch along the way also. Sometimes we did a dive south then one north which used up our SI on the ride.
The only way this does not work is the sites north of Karpata as it's one way and smart to stay on the paved road east thu Rincon and back to town - takes around 40 minutes. . There is a road just past Karpata that also returns south bu it's not maintained and rough even in a truck. It saves no time as it's slow going.
If you intend to dive the Slagbaai Park sites plan on just that for the day - rough road and slow going,
On the drive to Rincon if the Flamingoes are in they'll be at Gotomeer a short distance off that road - there's a sign. Or feeding in the salt pans south,
