You can define a payment threshold the moment that you click on "Settle all Balances". 

This opens a window where you can set the minimum payment amount. 

In this window, you can also opt to include or exclude affiliates who haven't set a payment method. 

If a payment threshold is set, affiliates must meet or surpass the stated threshold in order to appear in the payment file being generated. If they do not meet the requirement, they will not be included in the Payment file.

Automated payout: In the case that you choose to enable automated payouts, we recommend that you set a payment threshold. Automated payouts can be done through the triggers feature. You will likely need a developer to set this up for you.