First, if possible, you should wait until you have actually received your first refund.  From the information, you have given it seems likely that you had a refund originally, now you have to pay back some of that refund with the Form 1040X, but this still leaves you with a refund on the revised Form 1040.

The IRS recommends people wait until their original return has been fully processed (i.e. refund paid) before amending to ensure that there aren't any further issues with the return.  So, once you receive your refund, you can then send a check back with the amount due on the Form 1040X.