Hi jimboidaho. Welcome to SitePoint.
I'm not totally sure I understand what you are describing (feel free to post a link) but try adding something like
clear: both; to your footer and see if that helps. Floated elements are taken out of the document flow, so other elements can sort of stop seeing them unless you take a few precautions.
Another option (my preferred) is to wrap the two floated columns in a container div and apply
overflow: hidden; to that container. That prevents any following, non-floated items from slipping under the columns too.