Don't confuse indexes, source groups, search scopes and content sources.
Search scopes are built off of source groups, not index files or content
sources.
Here's the most granular way to do this, without having to worry about
index files.
1. Create four content sources - two of them will be for the sites
directory and two for the sites direction areas (one each).
2. Place the two content sources (one for the site area and the other
for the sites directory) in the same source group. Do the same for the
other two, but in a different source group.
3. Build your search scopes and away you go.
Now, the gotcha here is something that I just learned today: the sites
directory content source does *not* crawl the sites directory area in a
portal. Instead, it crawls the sites that are listed in the Manage
Sites to Crawl page. It is the portal content source that crawls the
sites listed in the Sites Directory.
I was *stunned* today. But I tested it and I'm 90% sure I'm right on
this point. I'll post something to my blog soon about this. So, in
effect, if you want the Sites Directory content source to crawl all of
the sites, then they need to be listed in the Manage Sites to Crawl
page. By default, embedded sites are added to this page, but if they
are not, then they are not crawled by the Sites Directory content
source.