Hi Jill
Please refer to the user guide for High Speed Data Converter Pro, available here: http://www.ti.com/lit/pdf/slwu087
Section 3.6.3 describes the Two Tone setup and display.
The ADC Input Target Frequency and ADC 2nd Input Frequency boxes must be manually populated according to the sample rate and signals you are applying. In your case you will need to enter the first Nyquist zone frequency locations of the input signals you have.
You had previously stated that your input frequencies were 2500 MHz and 2475 MHz. At 4000MSPS that would correspond to entries of 1500 MHz and 1525 MHz in the first Nyquist zone. However your plot above indicates that you may now have different input frequencies.
Regardless, once you enter the proper frequencies the FFT calculations should update for all of the two-tone combinations listed.
Best regards,
Jim B