Hallo,
You could use Master-Timer or the EPGsearch plugin (or vdradmin ?? not sure) to auto-programm timers. That way you can decide where the recordings are stored from the beginning.
http://mt.citd.de/ http://people.freenet.de/cwieninger/html/vdr-epg-search__english_.html
Or you can use AutoCutter to move them while cutting (German site, but Englisch README) : http://www.vdr-portal.de/board/thread.php?threadid=34583&sid=
Greetings Christian Jacobsen