I believe it is not necessary to have quota trees in order to have quotas. But it is highly advisable. I highly recommend putting all user home directories in quota trees. If you don't want to make false barriers, put all the users in a single quota tree. This will prevent a disaster. It's possible to have a disaster (well maybe the word is too strong) if your filer fills up. If it fills up, you could truncate an essential file such as /etc/passwd. If the quota tree(s) add up to slightly less than the entire volume, then users will never fill up the filer.
Unfortunately, if existing directories are NOT in a quota tree, you have to move them into one. This can be extremely time consuming. I don't know a way around this. You may have to have a night where the filer is unavailable to users while you make the move(s).