>How can I inform my application of which site is running it.
don't follow there...

>Do I have access to the users local hard drive when running WTS, if so I can write some setup data there.
we use Citrix client; and yes; you have access to local drives; only while the session is connected; if they start a lengthy process; and just close the TS session; it no longer has access to the local drives.

I've noticed that it takes a minute or two sometimes to "connect" to the local drives; so they aren't always available right away.