When you create a site, you have an option of whether to have this site
searcheable or not. If you check this box, then all searches at the
portal level will include the contents in the site. But when you are in
the site, you cannot search contents in the portal.

I don't understand what you mean by "I can't for the life of me figure
out how to put a search box into the Marketing Site". There is a search
box for every site, but you can only search for contents within that
site.

Thanks for the info. I solved one of my problems since originally
posting. The account I created for the Sharepoint Server didn't have
permission to search the documents on the main portal but I created
the new Site with my own credentials and that was why I could search
my new site but not the information I put into the primary portal.
(Okay, I do sometimes have my Homer Simpson moments.)

This is mostly academic now since I really want only one site rather
than several but I'm still confused about the search. Is it template
specific? The new site I created used the documents template but it
doesn't have a search box like my main portal and doesn't have an
option to put it in as I think I saw in other design pages.

Please read my previous reply - the difference is a "site" is a WSS site and
uses the WSS search which uses different technology and has different pre-reqs.
If you are not runing on SLQ with Full Text indexing enabled the search box will
not appear.

Crawling the portal should be as simple as running a full index on the OOTB
"Portal" context. As for getting a search box in your site - what DB are you
using? The search box inside sites  uses SQL Full Text searches (WSS's search
technology) instead of the portal search, so for this to appear you need to be
running SQL instead of MSDE and have full text indexing enabled.