You might try using a policy to set permissions back to inherit but there is a cool free sharpoint tool to help you manage your site permissions accross your farm. The tool is called Sharepoint SUSHI & a free download is available here:
http://sushi.codeplex.com/wikipage?title=Security%20Reports. There are other tools out there to help manage permissions amongst other things, but this tool generates reports for free! Can't beat that in today's economy.
If you decide to use a policy, there is alot of information available on the web & lots of tutorials on setting one up for the first time. Policies are really the way to go as they can stop site administrators from deleting permissions that you want to keep intack etc.
Permissions & heiarchy really are the foundation to a healthy farm. Good luck with this. :)