Sorry for the late reply here. The answer to your question is a definite YES! If each marimba is assigned to its own midi channel, this would be no problem at all. Having separate parts using different marimba patches actually creates a more varied, richer sound, and you'd have independence to set one part to 'shafts' and the other to the normal setting.
I am wondering if is possible in Finale 25 to use two different modulation wheel settings at the same time for playback. Specifically, I want to have one marimba part played normally and the other marimba part played with the shafts. I have no issues getting this to happen to all parts at the same time for playback, but am not sure if/how it is possible to have individual staffs read separate controller information. I am using a mac. Thanks for any help.