How to create VCS for two different repos?

Hello guys,

I have a virtual environment setup in Pycharm. I have two folders in the project that i would like to have two separate repositories on github. 

How can i accomplish this in PyCharm? 

To give you some background, currently i have been able to create a VCS for one folder in my project that is set up with github repository. But when i try to add second directory under the Settings >  Version Control 

I get this error: 

The directory C:\Users\Nermin\Desktop\EA-Monthly-Report\RetreiveReport is registered as a Git root, but no Git repositories were found there.

Thank you for your help,
Best Regards