Okay I figured this out myself. There was an Alt. Sales field that was disabled on all of our custom transaction forms, it simply needed to be re-enabled using Customize, it was a sublist line field. I can also set the ASA using script, if you look in the Records Browser under Sales Order you will see an 'altSalesTotal' field. This is the field you can utilize to make changes to the ASA. The ASA will now work with the Quota, Forecast and Commissions module as intended.