To set a custom payout amount, log into your PEGA-Pool account and then click on the Account Settings link on the top-right side of the website (click on your account name to open the dropdown). 

Next, scroll down to the Mining Accounts area. There you will see all of your accounts. Click on the specific account that you wish to set a custom payout amount for using the Edit & Setup Payout link. 
On the following page, scroll down to the Payout Settings area. Make changes to your desired payout threshold within the box provided.