Well it is less hard as you think, there are a lot of geeks out there on youtube trying to explain it. Just be a bit careful of those fanboying or girling to much over a certain brand, but yeah it is definitely worth to put some time into it. Most prebuilds it looks like the margins are made on the parts and not man hours put in, so if you want bang for your buck you better specify the parts.
Edit: Some easy starting places which will give you decent information plus ideas of what you could build and what is good value for money and also lots of comments of users are Tweakers.net (Dutch) and Bob's hardware.