I’m afraid by using raw .py files you’re going against what PyInstaller does. It compiles you .pys to .pycs then bundles those into a PYZ archive so that there is a) no folder containing your scripts and b) even if there was, the scripts would be pre-compiled.
That being said, it should be possible (although not really recommended) to do this. You can tell PyInstaller to add your encrypted Python scripts as data files by adding them to the datas=[] in the spec file (please do not debug in onefile mode). Exactly what you put in there depends on how you’re importing your encrypted code - whether files are loaded using Python’s import mechanisms or read from file, and where these scripts are located relative to main.py.