While a Biodome protects against the harsh environment, all buildings constructed still require the materials needed for the harsh environment enclosures. This is so the harsh environment enclosure can quickly be deployed in case of biodome failure.
Under sea cities are enclosed like cities in unbreathable atmospheres. The enclosure beams and columns are much thicker and textured with a coarse concrete pattern.
Town square can be built in the sea if the water is deep enough.
Roads can be built in the sea if the water is deep enough. They cannot transition between above water and below water. Cities under the sea cannot be connected by road to cities on land.
Buildings can be built in the sea if the water is deep enough for the harsh environment enclosure. The height of the enclosure is tall enough to fit the tallest building of that type made from its current material, just like on moons. That means the material will affect the minimum water depth required for each building.
Biodomes can be built in the sea if the top of the dome does not breach the surface of the sea.
Ship yards will spawn submarines just above the building, within the bounds of the building site.
Wharfs will produce fish and they will connect under sea cities with other cities that have a wharf.
Under sea cities are treated like other cities in an airless environment. Air must be imported/manufactured.
Spacecraft will land at the airport of an under sea city. If the tarmac is not enclosed, they will probably suffer a lot of damage from the sea while sitting there.