On the help cbp website for your interview it tells you bring valid passport. if you travel using more than one passport being them all to the interview so that the information can be added to your file. this provides you with the ability to use multiple passports at the global entry kiosks.
I was able to update my non GE passport online but when I used it in MIA they told me I needed to update it in person. I went upstairs and had it updated and now both passports appear on my GE account. My Non GE passport was used at the kiosk and I was instructed to see the CBP officer and was on my way in 10 seconds. I am required to use my non GE passport because it has a B1/B2 visa and I am not supposed to use my GE passport with an ESTA. The Kiosk did recognize my non GE passport. Not all CBP agents agree that I can use the kiosk with the non GE passport but the instructions seemed clear to me. I am sure US citizens cannot use another passport at the Kiosks. It would be nice if you agree or not that my interpretation is correct. help.cbp.gov/s/a