Zen theme duplicates menu

I’m trying out the Zen theme and made a sub-theme.
I need to make a menu do dropdowns, and other neat snazzy things that make them appealing.
Hmm, OK, I’ll load up nice_menu or super fish. However, Zen is going to put its own menu in the content area, so I get a duplicate menu, one added in blocks with the style of the module and another one that is pretty ugly in its raw state put in by Zen.
For the life of me I have not been able to find out how Zen is building that menu in order to control it.
I’d love to know how I can prevent it.
Or do I have to figure out the raw JS, CSS and build it into the SASS? Pointers for how Zen works (not in the style guide that I’ve found, just style guide stuff), sam

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