Group Policy vs WSUS Settings

Ok, how do I workabout this?: Windows XP client (branch) log on to its Windows 2000 domain (HQ)for its services eg, email, intranet, etc. I have deployed WSUS in the branch and HQ deployed SUS. I have tweak the client PC registry to point to branch WSUS server. Everytime the Group Policy sync, it will point to HQ SUS.