Yes, that's the most common way it's done in American kitchens. Stuffed peppers are usually set upright in a baking dish, often with a little water or broth in the bottom, and the sauce is either spooned over the tops or poured around them so the peppers sit partly submerged. Many cooks cover the dish with foil for the first 20 to 30 minutes at around 350°F (175°C) so the peppers soften, then uncover to brown the filling. The sauce keeps the peppers from drying out and gives them a braised flavor as the pepper walls soften.
A few variations you'll see:
- Sauce all around: the classic American version, peppers nestled in marinara or tomato sauce, sometimes with a little cheese on top.
- Sauce on top only: a lighter approach, with the filling holding the tomato flavor and the pepper skins staying a bit firmer.
- Par-boiled peppers: some cooks blanch the peppers first, which shortens the oven time and gives a softer texture, though it's optional.
If you want the peppers to hold their shape better, a thicker sauce works well, and you can use less liquid. I'm answering from general cooking practice rather than a specific study, so treat these as common approaches rather than rules.