We owe Federal taxes this year...When filing we opted to pay by check. Can we change method of payment to take advantage of points/miles etc?

Have you already filed?

Yes

Unfortunately after you have filed there is no way for you to change your payment method. Sorry about any inconvenience.

That is sad... Can I not amend or change the return so that I can pay online?

If you amend then yes you can but remember amended returns do have to be mailed in AND they can take up to 16 weeks to be processed, accepted and come back to you.

Okay, I found online a service to be able to pay my taxes online<a rel="nofollow" target="_blank" href="https://www.officialpayments.com/fed/pc_step_fed2_amount.jsp?exp=1">https://www.officialpayments.com/fed/pc_step_fed2_amount.jsp?exp=1</a>  Should I not be able to pay it through them and not have to pay by mail?