A picture can say thousand of words..
So you do not have SEPM (SEP Manager) installed on the server. SEPM uses IIS SEP client do not use IIS and it has nothing to do with IIS.
It will not remove Default website. Here The Default Website has been Renamed as Administration WSUS.
So your Administration WSUS is your Default Website.
So now coming back to your Actual Issue :
Was WSUS working fine before Installing SEP client ?
In SEP client do you have all the components installed or only Antivirus and Antispyware ( All Components mean Antivirus antispyware,Proactive Threat Scan and Network Threat Protection ) you can see this by opening the Client interface.
Network Threat Protection is a Firewall +IPS so it might be possible Firewall is blocking content update.
After Disabling SEP does your WSUS work properly ? Un-install SEP client , reboot the server to check if its actually SEP blocking automatic update or it is some configuration issue with WSUS.
Do you see any WSUS related error in Eventviewer ?