For layout I always start with a pen and paper, and sketch out a few ideas, then mock up my favourites quickly in an image editor. After looking at the ones on screen, and getting a few other opinions I'll go with one and get a full mock up, then get to coding it. If you want comments on mock ups, then feel free to post them here, no-one's going to be mean about them, and a second opinion is always a good idea. For picking colours, I hate to say that I'm perhaps a bit of a thief! Being semi-colour-blind, things which look good to me look rubbish to others, so I find other sites who's colour schemes I like, and adapt them to fit my purpose. ColorPicker plugin for FireFox is great, as you can click a colour on a page and it will tell you what the hex code for that colour is!
As to going with site first vs. logo first, it depends on the situation. You might have just paid $1000 for a killer logo design, then you're probably going to stick with it and make the site work around it. Apart from this though, I usually like to make a functional and attractive site first, then look for a logo that fits nicely into it.
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