I want to continuously display some data that I receive in a Flask Server in a GUI that I designed with PySimpleGUI. Currently my GUI and my Flask Server are two seperate projects, what would be the cleanest/best practise method to connect them?
The way you "receive data" in PySimpleGUI will be inside the event loop.  Usually communicating with a GUI subsystem is through something like a queue.   
Use a timeout values on your window.Read(timeout=100) call so that it doesn't completely block.  This will enable it to read the queue or make a function call or do whatever it has to do to get the data.
How to receive data in a PySimpleGUI GUI?