Here’s my bash script for it, where the first argument to the script ($1) is the location of the new profiles.
rm -Rf ~/Library/MobileDevice/Provisioning\ Profiles/*
cp "$1"/*.* ~/Library/MobileDevice/Provisioning\ Profiles/
Basically, anything in that ~/Library/MobileDevice/Provisioning Profiles/ folder can be used to build with (and will show up in Xcode).
If you’re looking to stand up a CI system, I recently gave a talk on using Hudson for it, and put up some slides and notes over here. My email is on my site if you have any questions about it.