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 -> Customize Form -> Sublist Fields -> Check ALT_SALES.

Also Suite Article 9674 was correct that you can edit 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. Now you can write a script to automate the ASA or just fill it in manually. Once the Alt. Sales field is enabled, you will now be able to work with ASAs on the Quota, Forecast and Commissions modules as intended.