Responsive utility classes
Easiest way I can think of is to have a vertical left menu AND the collapsing Top Nav in your design and attach/use bootstraps responsive css.
Then just add classes of hidden phone, tablet etc (to suit) to your left nav and hidden desktop etc to the top nav
see: http://twitter.github.com/bootstrap/scaffolding.html#responsive
play around with that and hopefully it should be able to do what you want