yes the airline would go from outside the tank/water and attach to the nozzle by the mj output.
Good point nate, did not think about the algae.
As far as bad water, my situation was (i believe) I did a 30% water change with oxygen defficient water, everything got pissed off, my corals looked terrible and lucky nothing died. I could amagine that you could kill a bunch of stuff with non oxygenated water if you weren't lucky.
Also if something fell into the water and decomposed you would be doing a water change with amonia and nitrate filled water.....that would kinda defeat the water change. To be safe I would add airline to the mj's and do a quick nitrate test....but you should be okay