I made a mistake on my return and paid more than I needed to. I got a refund check ($120) but it's the wrong amount ($1.8K short). How do I amend my return in this case?

I realized my mistake right after I filed and the government accepted my return.  I was told that if they find a discrepancy between my entry and the ones provided by the investment institution which also reports to the government, they'd fix it and refund me.  I received the refund check in the mail but it was about $120.  If I correct my mistake in turbo tax, the difference is actually that I overpaid by $2,000.  I have not yet cashed the check but I don't know how to go about amending my return since they'd already sent the check.  If I send in an amendment will whoever reviews it see that there was a mistake and the total I overpaid was more than the $120 they sent to me?  Thank you in advance for any advice!