[thelist] Search engines and redirects

[April]

I'm working on dozens of sites which will have a URL like 
subject.domain.com, but will immediately forward to 
subject.domain.com/subfolder/index.php?x=etc.

I'm wondering about hangups around search engines and especially 
pagerank in google.  If I put up a .htaccess moved permanently pointing 
at the index, does anyone know if the links pointing at 
subject.domain.com will still count?

I'd appreciate hearing anyone whose done this before throwing in some 
gotchas or worked for me's.