Haha.
As long as I know it is in the .plist file that's fine.
Right, so when I change resolutions, a script that swaps the .plist files for that resolution would be cool.. bit annoying it means each resolution's apps will have different preferences.
What you should do is read Apple's docs on how window positions and sizes are stored in the user-defaults plist. There is a simple way of saving this data, that works for most apps. But most apps aren't obsessed about resolution changes, a point which you've brought up twice now without explaining exactly what you're trying to do, what your app does, or why you care so much about resolution changes.
There are any number of ways to store
your specific data in the user-defaults plist. These can be tailored to specific needs, but you have to read the reference docs to see how things work.
Switching plists with a script is bludgeoning the problem into submission with a very blunt weapon. You might get it to work, but it will hardly be a good use of the API.