IE6's handling of CSS has a lot of weird quirks that don't make sense. I tend to design for Firefox, and then debug for all of IE6's quirks.
This may seem a strangely generalized piece of advice, but using position: relative on block level items, even when you don't need it, has solved many problems for me in IE6.
Also, be aware a bug with floats and margins in IE6 -- if you float something in a particular direction (e.g. right), and then put a margin on the item in the same direction (e.g. right), IE6 will double the margin for no reason at all.
There are lots of these. Google IE6 and CSS and start trying to figure out exactly how it is screwing up your life this time.
(Can't wait until that piece of sh** is finally no longer used by anyone.)