"I am not sure how I can mix them together though."
Inside your GUI you can import the data (from file/s), process it by calling whatever functions you want (including your own), and then finally save the output data (to file). That is the very general answer to your very general question.
Don't panic. Take it one step at a time, for example where does the data come from? Inside your GUI you can add the functions that import your data, just like you would from inside any other function.
I recommend writing your own GUI following Rik's well-written advice given here:
Otherwise you can use the AppDesigner (which makes it simple at the beginning):
