You can change the location of the files the Stats search under the Preferences tab, Tournament Files Location (Fort Stats) at the bottom. Highlight the default location and overwrite where ot look for your files. This will be saved here, and will be here the next time you run stats, so either your save your files ot wherever you chnage this to going forward or be prepared to chnage this each time.
I have a 2008 file, a 2009 file and a Non-League file, so I do alot of changing here. Good luck.