Still paid taxes due despite amendment saying I had a refund. Will I get my money back?

Had you payment been applied to your account before doing the amendment? The amendment should taken into account what was paid with the previous (original) filing and be included as a payment when calculating your new balance due/refund.

You will need to contact the IRS for information. It might be easiest to set up an account with them.

IRS Individual Online Account  

• Taxpayers with a Social Security number or an Individual Taxpayer Identification Number can create or access their IRS Individual Online Account to get information they need to file their return.
• With an IRS Individual Online Account, people can:
• View balance owed, payment history and schedule payments.
• Cancel scheduled payments.
• Get transcripts.
• View or create payment plans.
• See digital copies of some IRS notices.
• View key data from their most recently filed tax return, including adjusted gross income.
• Validate bank accounts and save multiple accounts, eliminating the need to re-enter bank account information every time they make a payment.
• View, approve and electronically sign power of attorney and tax information authorizations from their tax professional. 

The amount you paid with your original tax return should be on line 16 of Form 1040-X in your amended return. If it's there, then it is already taken into consideration and it is included in the refund from the amended return.