First, there are two different ways to fly a NPA with FMS guidance. One is LNAV/VNAV, the other is IAN (NG only, at least in our fleet).
Our SOP for LNAV/VNAV is to select MDA in the altitude window and at 500ft above MDA select GA altitude. LNAV/VNAV doesn't level off at MDA except if the FMC procedure contains a level flight segment, otherwise it will continue down to touchdown, SOP for us is to immediately initiate a GA at MDA+50 if no visual contact. Raw Data monitoring is required unless we have two operational FMC, two operational IRSs and two operational GPS receivers (which we dont have on the classic). Of course we can fly all non-ILS approaches except RNAV and GBAS using the oldfashioned method of HDG SEL and VERT SPD, VORLOC where appropriate as well.
IAN is flown similar to a normal ILS except that we cannot use two autopilots (can be flown raw data, FD only or autocoupled, autocoupled is required with RNP 0.15 or lower unless in visual contact). So we select the GA Altitude and just leave it there. It allows flying of every NPA for which we have a procedure in the FMC using the approach mode.
GLS approaches are non-ILS approaches, but precision approaches nonetheless and the handling is exactly the same as for an ILS (of course you have to select the correct entries in the FMC).
All in all it would be easiest for us if we could use IAN on every aircraft and just fly NPA and ILS the same way, however sadly IAN is only available on the newest aircrafts in our fleet, the older ones lack it.