I've moved the minipanel from the bottom of the screen to the top with no problem on the default aircraft but on certain add-ons there is no reference to the minipanel in the panel.cfg file. Yet I can still open a minipanel when pressing "W". Where is it being referenced to? I assume there must be some default minipanel being referenced? Or I guess I could add a new Window view to each aircraft but that might take awhile.Suggestions?

If not explicitly declared in the panel.cfg, the "default minipanels" are in the FS9defaultpanelpanel.cfg file. It will automatically select the appropriate minipanel for the type a/c model that calls it.