This all really depends on the boat you are on, what position you are at on that boat, and the captain's word.
Pyra- One engie stays down on main deck, one on top. Top engie handles the balloon and the front guns. In your example, he better be shooting. If you are the bottom engie, you are repairing. The only real time I like side guns manned is when I'm not under fire, and you have a good opportunity to better our situation.
Goldfish- Unless I call for a side gun, you are repairing. 9/10 times, my front gun is getting the arc priority. I'll call for the gun to be manned if i wish it, otherwise, youll lose arc pretty fast to the front gun, and you'll of done nothing but turn the gun.
Galleon- Again, depends if you are on top or bottom. Top is always repairing unless we aren't under fire or I call for all guns to finish them off. Bottom engie needs to watch the turning engines, his guns, and fires. A good gunner can repair his own gun, and if special needs arise, i'll be the one to relay that.
Squid- You are repairing unless I call for the side gun to be manned. They are pretty high maintenance when you start using pilot tools, especially the engines.
Spire- Top engie shoots and watches balloon and main engine, bottom is repairing hull, turning engines, and main gun on occasion (usually fire).
Junker- This is probably the most confusing boat for an engie in this context. It depends heavily on the loadout, but a more general way of doing it is, the top side guns are first come first serve. If I call for port guns manned, if one engie gets there before you, you just got the repair job.
This is all pretty general, but hopefully it helps.