If you've been following our "debug and validate" method described in the chapter, then for all intents and purposes, your layout should look pretty spot-on between both the browsers.
In the event that there is a visual discrepancy between Firefox and IE, in most cases it's a box model issue arising because you're running in quirks mode in IE. Generally, box model hacks apply to pre-IE6 browsers (IE5.x) and apply to IE6 if it's running in quirks mode. Again, running in quirks mode is to be preferably avoided, thus eliminating most of these issues. If your markup and CSS are validating (which means you shouldn't be triggering quirks mode in IE, but I've had people swear to me their page validated yet quirks mode was being activated), you might rather "live with it" than try to sleuth what's causing quirks mode to activate.
Basically, IE 5.x and IE 6 quirks mode don't properly interpret the box model standard. So, it will squish your borders and padding...