Does IE not like height:#% when you specify the position:absolute attribute?

In FF it displays the way I want it to however in IE it's messed up..
http://www.worldincode.com/page/index.cfm (ignore the color choice -
it's for distinction only)
What do you reccomend when wanting to make a website with a
header/footer/left side nav?
ems? pxs? or percentages?
Here's what I'd like to see in the end. layout :
http://www.worldincode.com/page/layout.gif
Can someone take a look at it and see if I've over/under doing it, or
if it looks right.
I'm having problems with positioning once below the header.. it's
giving me headaches.
I'm kind of curious as to why you'd pick one over the other? I know
that with regard to font-size (ems change in regard to the user
changing the font size on the client browser and pxs dont)
But what about when specifing height of elements.
I'm definitely a n00b at CSS.. I mainly deal with code behind the
scenes but I'm really wanting to learn how to design the front end.

Your assistance is appreciated
-- 
Auxilium meum a Domino
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