You will still get the first original refund. Then the amended return is only for the difference you get back or owe back. Amended returns can only be mailed. It will take them 8 weeks or much more for the IRS to process them. After 3 weeks you can track it here,
https://www.irs.gov/filing/individuals/amended-returns-form-1040-x-/wheres-my-amended-return-1
