What is the preferred way to structure and build OCaml projects?
Personally I'd give +1 for ocamlbuild. It's default rules are good enough to compile small to medium projects with one command and none to very minimal configuration. It also enforces some very reasonable conventions (not mixing sources with build results). And for larger projects it can be customized to one's desire, with extra rules & plugins. At the company where I work we are using it for a large project (Ocaml + some C + some preprocessing + ...) and it works like a charm (and gives us much less headaches than Makefiles would).
As for manuals, I'd think the user guide (available from the author's webpage,) should be enough to get you started. More funky stuff may require a bit more digging.
You've got a thorough listing of the options available, but this question will not have a clear answer. My personal recommendation is also to use ocamlbuild. The myocamlbuild.ml file provided here is a good start. It will allow you to easily compile projects that depend on various libraries. I don't think it handles the case of binding to C libraries, but there are additional examples on the wiki that may help.
Some people object to ocamlbuild because it is yet another build tool, complicating package managers jobs. However, its ease of use and the fact that it is included in the official distribution is making it more and more widely used.
You can also skip all this and use oasis directly. It is very new, and a stable release has not yet been announced, but it is very usable. It will generate the myocamlbuild.ml automatically for you. This is probably the way to go in the very near future, if not already. Furthermore, by using oasis, you will immediately have the benefit of oasis-db, a CPAN like system for OCaml that is under development.
Regarding managing libraries, the answer is ocamlfind. If you have multiple instances of OCaml installed, calling the appropriate copy of ocamlfind will automatically cause all references to libraries be those for that particular instance, assuming you use ocamlfind systematically for all libraries. I currently use godi to install OCaml and libraries. It uses ocamlfind, and I have no problem having multiple instances of OCaml installed.