There is no best way.
There is only one way.
One update at a time; one machine at a time.
It's not a limitation of Patch Manager; it's a limitation of the servicing stack used by Windows to install updates.
Which is one of the reasons the message in this article from a couple of years ago is still as every bit important today as it was then.
It may be possible to script the removals using WUSA.EXE