I signed up to pay my taxes via installment plan, using auto-debit. But I was also told I need to print a voucher and mail payment. This seems contradictory-- what to do?

If the voucher is for the full amount of taxes due, then that is just the program automatically producing the voucher for payment and you can ignore it and the instructions as long as your agreement gets approved.  It does this just in case you decide to pay it in full after you make the installment agreement request (and its also for your records so you have a record of your total payment due).  Also, while rare, it is possible that the IRS could deny an installment agreement request and then you would want to have the voucher for payment.

If you told the program that you were going to make a payment (i.e. your first installment) with your actual tax return and it is a blank voucher or just for the amount of your installment, then you can use it for your first payment.  But, most people don't do that and it is probably the first scenario above.

The voucher that I was prompted to print is pre-populated with my down payment amount I agreed to pay with my tax return NOT the full amount due.  Which is why it's confusing, am I supposed to make that payment by mail with the voucher and a check?  Or will they be taking it out of my account by direct debit?