This is a question dealing with response spectrum analysis. I know that if a force is applied in the response spectrum load case, it will be converted to a mass that will in turn affect the modal response. My question is, will that input force still be applied as a static force in the analysis? Or, would I have to apply the force in a different load case to account for it?

Response spectrum analysis is a dynamic analysis based on ground motion spectral acceleration. The acceleration usually varies with the period. Since there is no direct input for masses, what you are entering as forces are weights, and STAAD extracts masses from those weights. Hence, the same weight value should be entered in all 3 global directions for general space structures in order to get the natural modes and frequencies correctly.

The response spectrum result will be an absolute unsigned value for each output quantity which represents the maximum value for that quantity. Because of this, the 6 force/moments at each end of a beam will all be positive. Also given the member forces/moments on one end, you cannot compute those results on the other end because the values are considered independent much the same as if these were peak values in time history that all occurred at different times.

If you want static loading results combined with spectrum results, then use load combinations, possibly with the SRSS option.