Ok so I created two new GPO's for WSUS, one linked to each of the two Site OU's. Each GPO specifying the WSUS server i the respective site.
Currently each GPO is linked to the respective OU, and has Authenticated Users in the security filtering.
I forced a Gpupdate on a workstation in the MI ou and I see the 'MI workstation Windows Updates" GPO has been successfully applied. I run an rsop.msc and there is no 'Windows Update" section listed under Computer Configuration.
My GPO is not empty by any means, and since it was successfully applied why can I not see it under RSOP?
Also if it help, on the WSUS server under unassigned computers there is nothing, empty. My original problem is that computer group being empty is what led me to testing the GPO.