I had to file a amendment and my fees originally were to come out of my refund. I now keep getting emails asking for payment. What am I to do.

Even with an amendment, you should still get the original refund.....you shouldn't file an amended return until that original refund is received.   Did the original return ever complete processing?

Why was my bank account auto-debited for TurboTax fees?

When you filed your 2018 tax return, you chose the Refund Processing Service (aka pay-with-your-refund) which lets you deduct your TurboTax fees from your IRS tax refund instead of paying them with a credit or debit card.

Per the Refund Processing Agreement, you authorized us to debit your bank account if your refund was insufficient to cover your fees:

In addition, by clicking the "I Agree" button below, you electronically sign and authorize Intuit (through its third party processor) to debit the TurboTax Fees, Additional Products and Services Purchased and any applicable sales tax from your bank account number identified in the Agreement below, in the event that you do not receive a tax refund that is sufficient to pay for them.

Before we debited your account, you would have received 4 emails from us:

1.    An email with instructions to pay your TurboTax fees (minus the Refund Processing fee, if any) online by a certain date.

2.    Two more follow up emails asking that you either pay or request a deferment to prevent the fees from being automatically debited from your bank account.

3.    A final email letting you know that we're debiting the fees (minus the Refund Processing fee, if any) and that the auto-debit process cannot be stopped.

You can also be auto-debited if you signed up for Refund Processing and your refund is sufficient, but the IRS is still holding your refund 36 days after your original estimated refund date. In this case, you'll get the same email notifications from us, except we will debit the Refund Processing fee (if any) in addition to your other TurboTax fees.