To me, it looks like you need a field called "put in subfolder with name:" in the Save as dialog where you can specify the folder name required, because then you could use the {folder} variable to make PM put all the lo-res jpegs it generates in a new folder called (for example) "{folder}_lo-res". When you press 'Save' in the dialog the Finder would then ask you for a destination, but PM would create subfolders as required. If PM could do this you could open all the original jpeg folders into a single contact sheet, select all, and save as, and you could leave it alone.
This feature would also be useful in the Copy dialog, to let you specify a path to a folder, rather than have to use the Finder's save dialog.