Although the system as we have it right now is functional, I want to perhaps present a better option.
As it stands, we currently have a system where structures such as air pumps and heaters and coolers and such are installed directly into a room, with air vents being set up between bulkheads to cycle air between spaces.
This is functional, but necessitates a heater and cooler and fresh O2 and N2 cans in each area you wish to have a closed atmospheric loop, and also means venting heat from a centralized area that does not have easy access to vacuum is difficult.
What I propose is a system similar to conduits, called ducting, that can have switches to disable flow in one direction or another. Vents would need installing in each area the atmospheric system needs to reach, but this would allow for a centralized "atmospheric space" inside of a ship responsible for cycling and controlling the flow of air throughout the ship, and make setting up closed atmospheric loops easier.
Similarly, thermal transfer from a central point on the ship is rather difficult, especially if the space is surrounded by rooms.
Coolers are wonderful and all, but it would be great if we could have thermal conduits to extend their range.