You might be able to get what you are looking for by creating a calculation that does separate running totals for each type and subtracts the two:
Running_SUM(sum(IF Type = 'Sales' THEN [Amount] END)) - RUNNING_SUM(sum(IF [Type] = 'Quota' THEN [Amount] END))
That worked perfectly. I just needed to divide your calculation by quota and I had the perfect deviation from quota.
I really need to learn my table calcs. They seem VERY useful.