There is no real beginner's guide per se, as it usually is centered around modding particular watches to fix flaws, or doing major things like fitting pocket watch movements in vintage PAM cases.
If you go to the Rolex section, there is a beginner guide to modding a Seadweller that might be a good intro to modding. I reposted AJS' post on swapping movements linked in my sig...Francisco has a section on mods, and of course El Zigmeister posts regularly on his mods.
If you are looking at a specific brand or mod, you can start asking questions and you'll get some better responses.