Sounds like someone could use a newbie's guide! Fully illustrated Wrye Bash for Dummies. You were not alone, when I first got it I was utterly lost in all the features it had, and I didn't even have the newbies guide because it wasn't written yet! I had to self-teach myself everything about the tool, good thing I'm a quick study! I will say this, though, it gets A LOT easier as you learn, trust me. Now, I swear by it, and am using almost everything it has to offer.
By the way, I'm also using a whole slew of advanced tricks to keep my game up and running at a decent performance. Maintaining a 100+ mod load order is not easy, but to me is half the fun of playing this game. Bash is only half of my wizardry.
For this reason, you often see me hanging around the Oblivion Mods forum down on BGS. It's the best place to go for the most up-to-date info on modding Oblivion.