Subscription box credits are added/subtracted from the member's Subscription page/Due [subscription payments/make payment]
Deliveries are added if the subscription is manually created by farmer and the member has paid. Select as the payment type check (the default.)
Deliveries can also be added, via the direct credit payment type, if you want to Advance some boxes (while waiting for payment) or if there was a problem and the member needs to be reimbursed for a delivery.
Deliveries are subtracted if the member has been refunded (by the farmer), or if a box was given to the member before CSA Manager started counting deliveries. (Subscription start date is next week, but member given box this week.)
NOTE: If a pay-by-check order is placed by a member, when the payment is posted in the member cash account all the paid box credits will be 'released', or assigned to the subscription. No need for you to do anything else.