The bow mount setup will give you the ease of operation while fishing by yourself. Then you'll need a stripping basket of your choice, or, my preference is a piece of netting draped over the trolling motor to keep your flyline from hanging up. This system will cost approximately one-third of the other system, and would probably be more functional and allow you more control for your usage. The reason I recommend the Trolling Thunder batteries is because you have more power with less weight in a smaller size than two 12-volt batteries rigged in series. A boat with stern mounted motors will never be as maneuverable as one with a bow mount.
Guides use stern mounts for more power, and because they can steer with their pushpoles.
Flies don't necessarily have to be exact copies of each individual species, but rather mimic them all in profile and size. Baby herring aren't as colorful as the older and larger adults, being fairly translucent. Epoxy minnow type flies can imitate this well. By way of the same website, the Coral Sands hotel offers trips with Bonefish Joe, and both Woody Perry and A-1 Broardshad in Spanish Wells advertise that they take people bonefishing. Obviously there are guides to be found, but you will want to take everything with you that you might possibly need, such as extra fly line, leader material, plenty of flies, and so forth.