I'm using K-Patchmanagement for any of my clients. Some of them uses Windows Small Business Server 2008 with its integrated WSUS. How do you manage that?
use WSUS or turn it off and use Kaseya Patch mgmt. You can for all purposes use Kpatching like WSUS,
recommend setting up file share on server to act as Wsus and set up kpatching to download and pull patches from there. Just make sure the drive you put it on has enough space.
What i normally do is disable the GPO's for wsus in the server. Disable the update services service on the sbs08. Turn off all the auto sync stuff in wsus, delete existing content folders from patch downloads.
Then do the usual - disable the windows auto update in patch management. Use a LAN file source if its a big network etc.