I've never tried, but it might be possible to add the second US passport as part of your renewal application, just as one can add a second, non-US passport when doing a new or renewal application.

If you're unable to add more than one of the same document type, a US passport in this case, during the renewal process, you'd have to call to see if it's possible to be added manually. You'd need to go to an enrollment location to do this.

If neither is possible, you might run into problems if the US passport given to APIS is not the one associated with your GE membership. The kiosk would recognize you as a GE member but might not associate you with the passenger information that it gets from APIS. (I don't know how the back end works here.)