One is an integral antenna / receiver, the oft-recommended BR355. It's cable-tied to a bulkhead, about six inches below the foam-cored side deck. It feeds the VHF and the AIS, and the Watchmate AIS includes a screen showing GPS signal quality. Whenever I've checked, the fix quality has been excellent, with strong signals from a large number of satellites.
The other is a third-party RF antenna (non-waterproof, intended for cars) connected to a Garmin 128. Originally I had this sikaflexed to the underneath of the side deck, near the one described above. It worked about 90% of the time, but I did have some occasional prolonged outages. Not dangerous, given the number of other GPSes on board, but annoying as I had to plot fixes using dividers and ruler rather than the Yeoman . At the beginning of this year I moved the antenna to be pressed against the glass of the cabin window (but hidden from view behind some woodwork that passes over the window) and it has been reliable since then.
My conclusion is that modern GPS chips are fine below decks (as indeed are my phone and iPad) but the more primitive receivers of twenty years ago can struggle a bit. Although it is also possible that the cheap third-party antenna is to blame; I don't have an original Garmin one available to experiment with.