I dont know a whole lot about your site, and what exactly your looking for, but as far as things appearing ontop of other things, check out: http://www.w3schools.com/Css/pr_pos_z-index.asp
giving something a higher/lower z-index will make it appear above/below other things.
Or, if its not about it being on top, and you just dont want it to run that far, try adding width: to the menu's CSS, to stop it from going further.
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-Jaryth (UID590)