If absolute pressure, yes. The confusion comes from "corrected" baro readings for elevation. Say, when the weatherman in Denver says the baro is 29.9, it isn't really absolutely. He's correcting for the elevation, taking the lower reading (24.7 or so) and giving you an equivalent for what it "would be" at sealevel. They do this because the corrected number is more important and useful as far as weather predicting goes. Otherwise it would look like every mountain had its own "low pressure system" surrounding it.
So in short, if you obtain corrected baro numbers for your altitude (29 or something at 5000 ft) you should also enter the elevation into the program. If you obtain absolute baro numbers (much lower for higher altitudes) and use those, you can leave the altitude as zero in the program as the pressure takes care of it.
I hope that makes some sense. I'm not familiar with this particular program but just speaking in general. With any program you sort of have to figure out what input it's looking for so it corrects, but doesn't double correct.
BINGO. Absolute baro pressure, along with humidity and temp pretty much has you handled. If you are using relative, then you need to also use elevation. Good answer.