Amended 1040 change in refund amount

I filed an amended 1040X that resulted in additional taxes due.  My original 1040 had a refund.  When I printed out the return, I see I am supposed to mail a check for the 'amount due' -- but it is less than the original refund.  Do I need to send a check for the new amount due?  Or will IRS just deduct it from the original amount?

Note: I had originally used the direct deposit system, but the 1040x says send a check