I have looked at similar questions that may answer my question but I am still very unclear on how to go about the following:
I can create programs to run in the Python Shell in Idle and I can also set up windows with widgets in Tkinter, but whatever I create in Tkinter is pointless because I cannot figure out how to take my Python Shell code and "wrap" it in the Tkinter GUI.  
I have assumed that it cannot be done, and that entirely new code must be written to assist the language that is specific to Tkinter. I am very confused on how to create a well-rounded program without being left with just a GUI "skeleton" with random buttons, labels, entries, etc. and a Python program that is very unappealing and can only run in the ugly little Shell.
What you create with Tkinter is not pointless. It sounds to me like you're trying to compile a stand-alone program in Python, using the Tkinter library to provide the GUI. Once you have a script working, you can use a program to compile into a standalone program. Look into using py2app on a mac, or py2exe on Windows. Google them and see if that's what you're looking for.
Porting a Python Shell Program to a Tkinter GUI