Honestly, you really shouldn't have any problems with padding/margin, so long as you realize a few things. With Firefox, padding is on the inside of the div, and margin is on the outside of the div. This is not the case with IE.

I have a layout I'm working on right now that uses margins/padding, and it's the same in IE/FF, and I had no problems at all.

Honestly, the only cons you'll have with CSS will be VERY little and that's when it comes to making sure it's cross browser compatible with older versions of IE (5/6.)