You can use the same snippet (in this case you are using MenuBuilder) as often as you like on the same page, just make the snippet arguments different for getting different stuff:
<div id="mainmenu">
[[MenuBuilder?id=0&depth=5]] - gets the whole thing (if your document tree is no more than 5 levels)
</div>
<div id="sidemenu">
[[MenuBuilder?id=5&depth=1]] - gets a single-level menu of docs in folder 5
</div>
However, if you are using serious CSS styling, it would be better to use one of the list menu generating snippets that create a simple unordered lists with all sorts of options for id and class names for the list elements. You call them in a similar manner, specifying what folder you want to start with and how many levels, among other options, and then style the list in your CSS. My personal favorite at the moment is ListMenuX.