Jason Santa Maria has outlined his methodology hon how he designs websites. It's a good methodology, which he has dubbed “Grey Box”. What this helps accomplish is to break him from trying to design within the full-scope limitations of the medium (trying to break the design down into code chunks as he's designing, what's do-able with CSS, etc).
This is defintely not the only way to go about doing this. But it's a nice write-up on how he does it, and I always like to read on how other designers do their thing.