is that how it normally works?

unless u specifically write something in the css or js to override that

Normally this would happen, so you are probably using absolute positioning in your CSS, right?

Using your own theme?

Yes I had already made the site when I discovered c5. I just took that code and followed the tutorial on how to turn it into a c5 theme. I must not have done it right because when I put content that is bigger than the div it just overlaps the divs underneath and the footer does not move either. What do I need to change?

In your css, just set your elements' height attribute to auto, which is the default behavior for that attribute. As Maynar mentioned, if those elements are positioned absolutely, or if they're floated, this can be a little bit problematic, because they may not automatically expand the height of their parent elements. If you're using floats, you can fix this by using the clear:both; attribute on the following element. Do you have a link to your site that you could post?

Here is my site:
http://www.fblancaster.org

other than the broken links.. don't see anything overlapping (ffox3, osx, g5)