Hi what you need to do is create an Action. File – Action wizard – create new action. Then where it says start with, i would choose Ask when action is started. Then where it says save to, selct the Same folder selected at start, then click the options button on the right, then check the PDF optimizer button and click settings, modify your settings accordingly then OK and save the action. Now its a simple case of running the actions.
Could possible be tempted to test it first on a few files or test folder to make sure it works as planned?
Hope this helps?