The Mechanical Fatigue Tool (FT) is an entry level fatigue product. It cannot evaluate the fatigue damage caused by a constant stress (preload) and an alternating stress (external loading). You need to use Ansys nCode DesignLife for that type of calculation. From a fatigue damage perspective, the constant stress caused by the preload is a mean stress that does not contribute to the alternating stress. You could neglect the constant stress in the FE and include its effect in the fatigue damage by manually adjusting the S-N curve (e.g., using Goodman). This approach requires extra effort and would only be applicable to one mean stress, but it should work. You could make this approach more general (and conservative) by adjusting the S-N curve using the yield stress. This approach assumes that the entire model experiences stress alternating about a constant yield stress.