After you file

FIRST ... I cannot believe the IRS told you to amend a return when the original has not been fully processed yet.  Did they mail you a notice telling you to do so ?   If not  I would not compound the situation by filing an amended return as that could delay things even further.  You have 3 years to amend for the additional refund so don't be in a hurry.  

By trying to keep the amendment process simple for the DIY user this is not an easy thing to correct if you are using the ONLINE program.   You have the option to amend the return using the Downloaded option instead where you can  change that amount using the FORMS mode.