It's definitely an art - and a frustrating one at that!
There are so many layers of stuff involved that it's quite mind-boggling if taken in all at once. The tutorials help a lot though, as they lay things out in steps. 99% of the grief I've encountered is eventually overcome through experience - it's just a bit of a learning curve.
There are so many things that I know now that help simplify the entire process, but some of it is still just plain frustrating as Hell...
You should dig out that map project sometime MT - pass it by those of us into mapmaking and maybe we can help you get over the really rough parts!