If you change your Check Form (go to PR-Tools-Modify Check Forms) to Automatically Prefill Earnings, it will only show pay ID's with a current YTD amount. And the same if you pick to Automatically Prefill Employee Deductions. The only reason (I've seen!) to not automatically prefill earnings is if you want to show a formula. For example, Vacation Accrual Balance.

Sorry, I was (obviously) really tired on Friday. I didn't see the MyAssistant in the title. The MyAssistant task is probably using a Crystal report. You have to modify the Crystal report (in Crystal) and then re-attach it to the MyAssistant task. 

MyAssistant does not use your PR Check Settings.  The Direct Deposit design is independent from PR.  You will need to modify the crystal design.