You can stack at most one embarked unit with at most one naval unit. It is the same mechanics which allows you to stack civilian land unit military land unit.Do ranged attacks on a naval/embarked stack affect both units? Or just the naval one? I haven't gotten to a late game yet, but if the embarked are shielded, wouldn't an amphibious assault be super easy if you just bring, say, a battleship and a loaded carrier with a couple of embarked amphibious units stacked with them? Soften the city then take it with just one or two direct amphibious assaults. (Assume the opposing navy has already been dealt with.)
A naval assault is little easier, because melee naval units (like destroyers) can attack cities. So you can land and naval melee units, soften the city defence with ranged naval unit and then melee naval units and finally lunch an amphibious attack. Moreover, you can even capture a city with naval melee unit.