Most of the time using your local WSUS server is a very good idea - that means your getting your Windows Updates from a local server on your network. The updates install faster and it saves bandwidth for your organization (rather than have 100's of computers each download their updates from Microsoft over the Internet, you can have one or a few servers grab those updates and then your 100's of computers can download "locally").
However, sometimes the WSUS server has issues, or it doesn't have the updates you require (I have run into this trying to manually install .NET 3.5 onto some older servers). To bypass the WSUS server is relatively simple, however it involves using REGEDIT, so you must be careful (ie: I take no responsibility for you following these instructions - if you bork your computer, it's on you!).
- run REGEDIT
- go to folder: \HKEY_LOCAL_MACHINE\SOFTWARE\Policies\Microsoft\Windows\WindowsUpdate\AU
- change the value of UseWUServer to 0
- exit REGEDIT
- restart the Windows Update service
That should do it. I strongly recommend changing it back to 1 once you've resolved whatever issue caused you to want to do this.