"From what I have seen so far, it is the other way around"
Your observation is correct. In-App designer, you will first create graphics interface and then write callbacks and functions to respond to different events related to GUI. App designer is designed with the goal to minimize the need for code to create GUI itself, you can just drag and drop GUI elements, app inventor will create that code in the background for you. In this way, the user can focus on the actual features of GUI. It also helps in keeping code organized and minimize chances of errors.
"My intuition led me to think that you'd launch App Designer from the code you were working on, and then create the GUI to interface with the code."
To get started with App designer, you we need to have an understanding of these fractures of MATLAB
These resources will help you get started for advanced App designer usage.