The Factory Service Manual is really one of the only useful books you can use.
The way I've learned everything on mine is googling problems and happening to make sure I pay attention to the more logical answers coming from the more experienced forum users. Just getting info from the Internet doesn't cut it, you have to filter out the useless crap.
Through the Internet searching, troubleshooting and asking for help, combined with climbing under the Jeep every once in a while and looking around at what's down there, I've become pretty confident in my abilities and know how quite a bit of it works and how to fix it should something go wrong.
I knew absolutely nothing 5 years ago, I couldn't tell you what an alternator did back then. To date, I've swapped engines, transmissions, suspension, and will tackle nearly everything but gear work in the axles.
Helpful Internet posts and getting down there yourself and figuring out are the two best tools I've come up with.