Part of the problem in my experience is that there isn't a single, reliable cloning manual out there that provides start-to-finish logical guidance. Most people do their projects in an ad-hoc sort of way. If I have a particular cloning project, my resources are (in order) my PI, my labmates, the NEB catalog, and whatever I can google up.
You'll probably want a decent background in molecular biology -- equivalent to one or two intermediate college courses, or whatever you can self-learn from the right textbooks. Molecular Biology of the Cell is one of the better textbooks out there. There are some relevant manuals on cloning out there, but mostly they're concerned with the gory details on what biologists do at their bench. One is written by Maniatis. It doesn't really present a unified, logical approach, but is really just a collection of protocols and recipes for accomplishing individual steps, without providing much guidance for a whole project. Still, if you have access to a university library, it's probably in the reference section, and it has a lot of good information covering the basic theory of all sorts of techniques. Another good resource is the New England Biolabs website -- they sell reagents and kits for subcloning, and their technical references are excellent. So good, in fact, that their catalog was passed around one of my undergrad lab classes as a supplemental textbook of sorts.
The big challenge for you is to put all of that crap together -- distilling the accumulated lab superstition and hodge-podge of tools into a flowchart of decisions that outputs useful cloning advice.
Unfortunately, most such attempts are written by biologists with a bit of coding background... and end up being the crappy sorts of projects that I could do myself, if I wanted to put the time in. The better computer scientists making their way into biology are all going into bioinformatics, which involves big sexy problems like analyzing and comparing whole genomes. The routine concerns of everyday biologists haven't attracted the right talent.