Check [X] the Linear Transponder Tracking option if you are using a linear transponder such as HAMSAT / VUSAT / VO-52. These satellites receive a specific range of frequencies (typically 40 - 100 kHz) in one band, convert them to another band and amplify the converted signal for transmission back to your planet. The converted signal is inverted - LSB becomes USB etc. - this is known as an inverting transponder.
Do not use the satellite tracking built into your radio - let Ham Radio Deluxe do the work for you (for example on the FT-847 this is the Tracking option). To set up the linear transponder frequencies:
As you tune your RX frequency the TX frequency will be correctly adjusted by applying  offsets from the center frequencies and then  Doppler correction. To adjust your transmit signal so that it matches the receive frequency use the spin button to the right of the TX center field. It will be necessary to adjust the transmit signal as your radio(s) may not be correctly aligned, also the linear transponder in the satellite may also not be correctly aligned.
The tracking option in a radio cannot correctly compensate for Doppler, this is one reason why many QSO's drift gently across the linear transponder's available bandwidth. Only correct computer control will ensure that two or more stations stay on the same frequency while the satellite passes overhead. When using the linear transponder option Ham Radio Deluxe will correctly control your radio's frequencies so that are they are both compensated for Doppler shift.