As for an FAQ, you can refer to the Oblivion one: http://www.gamesas.com/topic/449239-oblivion-mods-faq/
Most of it still applies. Though, you need to replace to OBMM with NMM in there and add in the Steam Workshop.
I keep meaning to rewrite it for Skyrim but haven't gotten around to it...

Personally, I recommend you go with Bash for installation. You'll need BOSS to manage load order if you plan to use a fair number of mods.