If you mean that the $2,500 was the amount in excess of your RMD, the $2,500 was deposited back into the IRA within 60 days of the distribution and the $2,500 is included in the amount in box 1 of the Form 1099-R, this is a rollover. After entering the Form 1099-R, indicate the amount that was RMD, indicate that you moved the money to another retirement account (or returned it to the same account), that you did a combination of rolling over, converting and cashing out, then indicate the amount that $2,500 was rolled over. The entire amount will appear on Form 1040 line 4a but only the taxable amount of the portion not rolled over will appear on line 4b along with the ROLLOVER notation. Whatever amount was withheld for taxes, shown in box 4 of the Form 1099-R, will be credited on Form 1040 line 17 along with any tax withholding from any other sources and will either increase your refund or decrease your balance due.
Do not enter the $2,500 anywhere as an amount of negative income.
