Do I have to mail my amended taxes in order for it to change my original refund?

That is correct. Amended returns will not be available for the 2016 year until sometime in February. 

You should not try to amend your return until the original return it has been fully processed and you have received your refund or your payment has cleared.
Amended returns do not “catch up” to your original return and replace them; they are processed as two separate returns.  
Amended returns have to be printed and filed by mail.  It can take the IRS up to 12 weeks or longer to process them.   If you are due a larger refund than on your original return, your amended return should only show the difference and you will receive a separate check for it.  If you owe money on your amended return, it will show only the new amount owed, you will have to mail a check with the return. Click here for amending instructions: https://ttlc.intuit.com/replies/3288565