Hi Jordan, thanks for the css 101 but as I stated, I have to have a fixed height on my footer. That's that. It's totally normal to have a fixed height or width on a container. In this case I also know exactly how much content is going in the container and it will never have to change size. The problem is that on the backend your css makes some naive assumptions, that everyone is going to do things your way which isn't very user friendly.
Here's a link to the css I'm using to have a "sticky footer" http://www.cssstickyfooter.com/
If you make a template using this technique, set the footer height to 50px and then try to have one place holder on top of the other you won't be able to place content into the second place holder. Again, I can go back to SF 3.x and how it is still better than 4.0 this wouldn't have been a problem because in addition to drag and drop you could add controls by selecting the control, then selecting the place holder container from a drop down and then clicking add. If you think your css is perfect and can't change then maybe you need to add this type of functionality back so that content can be added to place holders where your css prevents it.