I fixed the overlapping submission fields problem at my classcaster blog by playing around with the template files. It seems (and I may have some of these details wrong) that the submissionForm php function pulls in the header.template and footer.template files from the template, but it neglects the main.template. This is probably so the two sidebars don't show during submission.
Well, my particular template needed a "<div id='content'>" at the start of the main body content to make all the CSS goodness render properly. Without that, it shoved everything to the top of the page.
My solution? I moved the offending <div> tag from main.template to header.template. It seems to have worked.