The number 1 best site on the Internet for computer parts is
www.newegg.com . They're not the cheapest (even though their parts are pretty damn cheap compared to most), but they have EXCELLENT RMA and return policies. If your parts come broke, you get a refund no matter what. They also have excellent tech help.
Putting together a computer is pretty intimidating the first time, just like you said. You need to know all sorts of things like which processor manufacturer you want to go with and which videocard company you want to trust. If you can give a price range of what the new computer can be built with, then many people here can give you suggested computer combinations.
You're already ahead of most people by knowing what RAM, hard drives, and videocards are. I think you'll be fine as long as you buy parts that are compatible with each other.
If you want to know specifics, just ask. Give us a price range, and we can definitely give our advice on the best computer for the money. You're making a good choice by building it yourself -- you'll get way more performance for the money.
My last question: are you gonna use this for gaming? Gaming computers are a bit different than the average computers. They're more expensive, but much more powerful.
-Lasereth