We just amended our return based on missing information and now owe less. Should I send the check for the original amount and then get the refund check from the IRS or can I simply send the check in the amended amount? It seems to make more sense to do it the latter way for many reasons but I wanted to check.
Because the IRS takes 12-16 weeks to process an amended return, it is probably better to send the original amount and wait for them to refund the difference.
You can track the progress at the IRS Where's My Amended Return? site, but make sure you don't check this site until three weeks after you've mailed the amendment.