Try
http://www.trainsimfiles.co.uk/ukfs_support.shtml. The manual is here (you'll need Adobe Acrobat Reader from
http://www.adobe.com/products/acrobat/main.html) as are another couple of useful documents for creating tunnel portals.
This manual is strictly speaking for UKFS version 1, but is still an excellent guide. I believe an updated manual was planned for version 3, but as far as I know it hasn't materialised thus far (I think Tim has understandably put most work on UKFS on the back burner until MSTS 2 makes its appearance for obvious reasons, but I don't know if the updated manual fits into this category).
If you have specific queries, posting to the UKFS forum is a good idea as Tim and other experienced users generally answer queries very quickly from there (browsing back through the posts there also yields a treasure chest of handy hints as well).
Paul