I'm the Polystyle author. To change PS to the formatting style you like, you can run the Polystyle Configuration tool. In Tab 1 are two options for changing your style. You can either use the Graphical Styler to change the style rule using mouse clicks or you can edit the example files directly. They are located in the Polystyle/examples directory and Tab 1 has a GUI for opening those files.
In the Multi-Edit/Polystyle integration it is as you describe and the entire file is saved and then passed to Polystyle to be formatted. Polystyle does create a backup of the file by default called <filename>.polystyle.backup.
Here's a link to the Polystyle help page:
Thanks and have a good day