Back in the bad old days, people used tables to do layouts for web pages. Actually, many still do, and if you design HTML emailers it is pretty much a requirement.
Anyway, you've probably heard that tables are out and CSS-styled div's are in. It sounds all very wonderful in practice (position stuff anywhere on the page), but in practice one needs to develop decent methodologies to actually use these capabilities to create a useful layout.
Here's a great article I found: From PSD to HTML
I am tending towards using Fireworks rather than Photoshop for a lot of my website graphic design these days, but the principles are the same. This article breaks down the practical steps very nicely, and the principles can certainly be applied to a WordPress theme as well.