These factors are not explicitly a Patch manager issue, you can play with the settings that microsoft makes available to you but PM doesn't itself directly control things like reboot behaviors associated with the windows update agent. This thread discusses the problems you are having.
Are you using WSUS or SCCM?
With WSUS all you can do is tell your updates to download but not install and then at the approved time you can use scripts to kick off the update installations, as discussed here.
If you have SCCM there is a feature called Maintenance Windows that allow you to have more control over the scheduling of these things.
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