Search Scopes.
Do you want to limit how far down they can search  or the width of the search.
That is, limit a search to a particular department or office? Where is the data
for the departments and offices  stored? Embedded site collections or standalone.
Either would work but I would hate to have to crawl data twice just to design
search scopes.

Yes, limiting a search  to a department/office. Each Office and department has its own area with sites (WSS) underneath.

I need to get some clarification of terms.
Areas (SPS) do not have sites. A portal  can have embedded sites. They are going
to be completely crawled by default so limiting the depth would be problematic.
So are the sites embedding top level  site collections within SPS portal or are
they standalone WSS sites associated with portal(s) or are they separate WSS
sites simply being crawled by SPS search?