"Random Vibe FEA on a spacecraft component."
Probably 90% of a rocket is not operational during launch, so you are in a very small segment of a small segment of the aero community.
" My question is once we have stress values from the analysis (either 1 sigma or 3 sigma), what then do we do with these?"
Compare them to failure criteria
" Compare to yield?" yes, that is one criteria.
" Superimpose with pressure and thermal stresses and then compare to yield?"
Yes, if the combined stress is a realistic operating condition. HOWEVER, remember that a pressure load on a thin shell fuel tank, for instance, provides a great deal of stiffening to that shell structure. You may want to simulate the combined loads (launch vib + operational) to make sure you don't end up overpredicting (or underpredicting) the true combined stresses.
" Are they suitable only for fatigue calculations, and again in combination with operating stresses from a separate analysis?"
Realistically, you would want to create some combination of stresses from 1 to 3 sigma as a "normal" launch environment and examine the fatigue margins as a result of that. I.e. it is not very probable that the part will see a continuous series of 3-sigma events, what it will actually see is a time distribution of events, the probability for each level of loading occuring during any given amount of time is equal to the area under the bell curve...etc. etc. With luck, you can reduce the number of cases you must analyze by using judgement, and reduce the analysis to a subset of "worst case scenarios".