We are using both WSUS and Patch Manager and have been for over a year now. We use WSUS to take care of any Critical and Security Microsoft updates. LANDesk then takes care of Adobe and Java updates and anything else that WSUS doesn't seem to do e.g. Firefox. We haven't run in to any problems so far.
It all depends on how you want to manage it. You can set up rules that will automatically approve patches based on the vendor name, patch name or severity level.
I tend to only approve updates in patch manager once a month, so as not to annoy our users with reboot prompts. I usually schedule this to happen a week after "MS Patch Tuesday"
If I had a choice, I would do it all in patch manager (alas, not my decision)