I would like to first print all of the paychecks in Mekorma and then print all of the Direct Deposit remittances in the same format. Is this possible?

If your preference is to print Direct Deposits with Mekorma formatting after checks you would leave the 'Suppress DD Remittances' unmarked at Mekorma System Options. 

In order to prevent the checks and direct deposits from getting interspersed:

1. Go to the Mekorma Area Page: Setup>Payroll>Checkbook Setup
2. Drill into the checkbook in question
3. Go to the Additional tab>Additional Features
4. Mark Activate Payroll Sort Feature 
5. Mark Sort Direct Deposits To End