Run a particular Python script as a Service
In Automator, use the "Run Shell Script" action. Normally, you would set the shell drop-down list value to "/usr/bin/python", to use the built-in python 2.7. However, if you select a unix shell, but make sure that your script contains "#! /usr/bin/ env python", or an explicit path to your python3 installation, then it should work.

If you select the other drop-down list "Pass input" to "as arguments", then you can get the filenames of your selected items from sys.argv().

Note that Automator already comes with a watermark action that lets you put one PDF on top of another. (It's also a python script, if you dig deep enough into /System/Library/Automator/)