From your description it sounds like you only want to display certain
levels within the active section of your site. It sounds like you've
figured out how to limit which levels are rendered, but setting up
your navigation templates correctly (using <navigation:nextlevel>
templates for the levels you want to skip over). To limit by section,
you need to make use of the selected / not selected toggle. Selected
means that the current page is in the active section of the site, and
not selected means that it isn't. So for all your
<navigation:nextlevel> templates set them to only work for selected
pages. This will have the effect of trimming your results down to
only pages in the active section of your site.
Best,
- Eric