You don't need to send a check/voucher for the initial payment of your direct debit installment agreement.  However, you will need to send a check (or just pay online) for any payment that you indicated that you would send with your return while preparing your installment agreement application.  

The program would have asked if you would like to send some payment now to reduce your balance and interest owed. If you chose to do this, then you would need to send that payment.   For example, if you owed $1,000 but you wanted to send $200 now and get an installment agreement for the rest, then you would need to send the $200 via paper check (or online payment) now before your agreement takes effect.  If you aren't sure, then you should be able to see on Line 8 of Form 9465 in your pdf any amount (if any) you indicated that you would pay now.

https://www.irs.gov/payments