If I owe the IRS after amending my tax return, can I send in a partial payment with the amended return and make the rest of my payments online?
Yes, you can. I would try to make all of your payments by April 18, 2017 to avoid any penalties or establish a payment arrangement with them via their website.
I have pasted the links to pay through the IRS website and to set up an installment agreement (if necessary) below: