Contributed By: Mohammed. Athif Khaleel [MVP SUS/ WSUS]
I would suggest you to install SUS in separate site and keep Share Point (SPS) or any other IIS Applications in the default website retaining the ANONYMOUS ACCESS on the default website. OR, you can install SUS first on Default Website & then install any other application on other sites, Procedure is the same;

Review these steps;

1. Before installation, open IIS Snap in.
2. Stop all websites.
3. Now run the SUS installer package.
4. Since no sites are running, SUS will create a new site for it.
5. Assign the site to run under another IP, and restart the rest of your sites.
6. Make sure you put a DNS entry pointing to the site.
7. Then set clients to update from this IP ADDRESS.

Happy Testing!
Athif
Mohammed. Athif Khaleel
"Save the Internet. Keep all Systems Patched"