Hello Chris,
When a new computer is managed by the SCE server, it is automatically added in the "All Computers" group. So SCE does not need to show the "Unassigned Computers" group as WSUS does.
Generally, you can only use the SCE console to deploy the software packages. Just ignore the WSUS console.
If there's any other issue when you deploy the software packages to the managed computers by SCE, please tell us.
Thanks,
Yog Li
TechNet Community Support
