Its been almost two years since I asked this question. I just came up with css calc() that resolves this issue I had and thought it would be nice to add it in case someone has the same problem. (By the way I ended up using position absolute).
http://jsfiddle.net/S8g4E/955/
Here is the css
#up { height:80px;}
#down {
height: calc(100% - 80px);//The upper div needs to have a fixed height, 80px in this case.
}
And more information about it here: http://css-tricks.com/a-couple-of-use-cases-for-calc/
Browser support: http://caniuse.com/#feat=calc