I can see some of the alignment issues you're having. Here's an idea though. Instead of using divs with overflow, which I take it is the solution you were considering, try this:
Take the bottom of the parent box and place it in its own div. Put the content in it's own container, and then nest the navigation and the content areas in their own containers and float them to each one's respective side. Clear the bottom of the container with the content in it, and run a repeating background straight down the page. Looking at the page, there's a repeatable graphic loop in there, maybe 10-15 pixels tall.
Now, when your content overflows the area, instead of unsightly scrollbars or a broken page, the content area will adjust gracefully.
Thanks very much for the tip, it sounds like a good approach for me to try out. Once I get some content ready to test with, I'll try out your recommendation. Yes, I have to admit that I'm relatively new to table-less design, so this was my kind of amateur approach to it which left me a bit perplexed as far as how to properly incorporate content without compromising the design.