I'm sorry for the vague wording in this question.
I've created a login system with Tkinter but am not sure how to create a new window for the main menu of the app I want to make.
I've tried opening a new window but that still leaves the login window open and if I attempt to delete it with the .destroy command it shuts down the whole thing.
is there a way to completely refresh/open a new window?
is there a way to completely refresh/open a new window?

The simplest solution is to put all of your "windows" inside frames -- login window is all inside a single frame, the main window is all inside a single frame, etc.
Then, when you're ready to switch from one to the other, just destroy the login frame and create the main window frame, all without having to destroy the main window.
A similar solution is to simply delete all of the children in the root window and then add the new widgets. It's easiest if everything is in a single frame, but you can destroy all of the widgets one by one by calling winfo_children on the root window and iterating over the results.
How to progress to next window in tkinter