The setting Never reboot after deployment is honored whether the a Shavlik\MS Scheduler starts the deployment or you start it by hand in the Staged folder. I ran through the steps moments ago and the machine I tested with did not reboot after the patches were installed. It's possible Windows Update is causing the reboots. Please verify these settings on the target machine: Best Practice: Windows Automatic Updates
Running these deployment by hand isn't a true workflow process so we don't have a easy method of monitoring the deployment on the client. This method is normal reserved for servers with special needs or troubleshooting. Deployments vary, but you could look for this line in the STDeploy.log:
STDeploy.cpp:249 Current remediation phase completed. Process exit code: 0.
You control which patches are installed by filtering from the scan. You can do this numerous ways through a Scan Template, the best method is to use a custom Scan Template and a Patch Group together to exclude specific patches. How To: Include or Exclude Specific Patches in Scan Results
Apologies for late reply,