The easiest way is to avoid working folders altogether, and do a recursive checkin, specifing the base local path and equivalent base VSS project, as demonstrated in the VStudio.bld sample ('Check In All Files' step).
If you need to use working folders for some reason, these posts might be helpful:
http://www.kinook.com/Forum/showthread.php?threadid=354
http://www.kinook.com/Forum/showthread.php?threadid=1