Message Filters - How to run on specific folders?

I have some mail filters to automatically move stuff from inbox to local folders. I now want to create some rules to periodically check those target folders for mistakes and move them back to inbox when necessary, based on keywords. I have set it all up, but can't see any way to ask the filters to run on specific local folders. Its weird, i can ask it to 'run now' on one specific folder, but can't see how to set the rules to always run on just one specific local folder. Is that possible? thanks