Is there any guide to the mechanics of Arcanum? There's a lot of stuff that just sort of... pops out of nowhere with little explanation (i.e. fatigue penalties, scars, the levels of CH required to get another follower, etc) and I can't find much info on that.
Go to the download section and grab the Arcanum manual if you don't have one already. It explains most of the concepts you've found confusing. There's also a strategy guide, but watch out for spoilers if you read that.