Beginning Thoughts:
Photoshop
Mock-ups
>>>see examples
on local drive/ download layout templates>>>
(you can also use Flash or Illustrator if you feel more comfortable in these programs). Basically the idea is to complete the design before you build the site. This is usually how it goes in the real world as well. Site design needs to be approved before implemenation starts. Often this is a lengthy process of changes in the design and resubmitting to the client for design revisions.
Once the site is approved. The architecture (structure) can be built. Final graphics and design elements can be prepped, and then put into the architecture.