OK so I figured out a bit more...
I had recalculated the quota for the new drive as per the HowTo, but I needed to recalculate the quota for the original drive as well. Perhaps this is because I mounted the new drive on /mnt/ and used symlinks from /home/e-smith/files ?
I ran:
quotaoff -vgu /dev/hda3 <-- original drive
quotacheck -vugc /dev/hda3
quotaon -vgu /dev/hda3
WARNING: This resets the quota limits for all the users!! I have only a few users, so its not big deal...
Now the reading in the quota pane shows the amount used on the original drive (I THINK, not sure but its close), it doesn't include the total from the new drive. Running quotacheck on the new drive does not solve this, nor does a reboot. Its as if Quota isn't configured to add the totals from the new drive, despite the fact the new drive is configured to use quotas in /etc/fstab
output from quota:
[root@morpheous ~]# quota -v mike
Disk quotas for user mike (uid 5000):
Filesystem blocks quota limit grace files quota limit grace
/dev/hda3 2500748 367001600 398458880 1526 0 0
/dev/sda1 27293620 0 0 79289 0 0
there is no quota enabled for the new drive (/dev/sda1)