I recently came across a very excellent blog post by Jay Kimble that contains step by step instructions on implementing Atlas into an existing web application.  I walked through these and found them clear, complete, and easy to implement.

So as you get into Atlas implementation or web development, you'll see there are two basic types of these you'll be doing - the first is to use the Web project template from Atlas, and the second is to try and wrap Atlas features into existing web applications.

I'm guessing that probably most of us that are going to use Atlas features are going to first try and wrap them into an existing site.  So these instructions from Jay will be very helpful.