The Minimum Payment Threshold refers to the minimum accumulated commission an Affiliate must earn before the Affiliate is eligible for payment.  Once an Affiliate hits the threshold,  their bill  can be generated in the Accounting area.  Once the bill is in the Accounting area, a payment can be initiated to the Affiliate.

From the Setup>Settings>Billing Settings>General Settings you will find Affiliate Minimum Payment Threshold.

By Default, the Affiliate Minimum Payment Threshold is set to a value of 0 (blank).
The Affiliate's bill will roll over from billing period to billing period and will be displayed in Accounting once the threshold has been met.
This Billing Setting effects all Affiliates unless the Affiliate's individual Card has been modified.

From the Affiliate Card>Home>More tab

The Minimum Payment Threshold can be modified for an individual Affiliate.
Placing a value here will override the Billing Setting for the individual Affiliate