If you were confused typing that... then I may have a bead on it :)
First depends on if the site really ARE two different sites. If not - and they are simply within the same site - you can do it. With the NavControl you can set the ParentID (I believe) which is the basis for the menu --- so if you had an About Us page (id 123) with a bunch of sub-pages --- you can set the ParentID to 123 and the menu will display only the sub-pages of that page.
So I think you could have your site layout like this:
- Home Page
- Site 1 dummy page
- home page 1
- page 1-1
- page 1-2
- Site 2 dummy page
- home page 2
- page 2 -1
- page 2 -2
Then have 3 skins - one for the Home page -- one for Site 1 and one for Site 2
Home page skin -- NavControl set ParentID to the home page ID and do not disply children
Site 1 Skin - Set NavControl ParentID to the Site 1 Dummy Page ID -- show children
Site 2 Skin - Set NavControl ParentID to the Site 2 Dummy Page ID -- show children
Only thing to note - Site 1 Dummy Page - should link to your site 1 home page --- and Site 2 dummy page should link to your Site 2 home page (page settings)
If they are completely 2 different sites -- then these are not the droids you are looking for :)~