There is a place to set the path globally, under Options/Setup. What you have done is set it for each group individually under group properties, which will override the global setting.
You have a good point that if you have a per-group download path set from V5 and upgrade, then change the global path using the new pathing scheme, it probably won't work unless you clear out the old per/group settings or change the per/group settings to reflect the new scheme.
The new pathing variables are documented here:
http://help.newsbin.com/index.php/V640_Pathing