I have been using PyCharm for a bit so I am not an expert.
How I normally ran my programs was with the terminal like so:
program.py -t input1 -t1 inpu
It was almost correct but just needed little correction with full script path.
Menu: Run->Edit configurations->"+" (add new config)->Python.
Run->Edit configurations->"+" (add new config)->Python
Script name: path + /program.py
path + /program.py
Script params: -t input1 -t1 input2
-t input1 -t1 input2