When captaining a Pyra I jump off the helm to fix the hull in a 1v1 slug fest. I would prefer my upstairs shooters keeping up their rate of fire than trying to save the ship. I try to time my departure just before the hull goes down and I go back to the helm just before the hull goes up (that way my engineer is assured the last tap with a mallet). If I time it right we can get the armor back before the last flack of the clip hits us. It is a highly situational move, and one that only works if the enemy is stationary (pyra v pyra).
In preparation to leave the helm. I burn moonshine on neutral for .5 of a second to cancel out any turning momentum, then if the engines are even I put the ship in a slight backwards velocity. This gives the highest chance of my guns staying on target while I am away from the helm.
The only time I gun as a captain is on the galleon when my side guns have target, and my engie is too busy with the hull.
I have also been known to fix the hull and balloon on a galleon and the balloon on a junker. I even go as far as fixing engines if they are all down and there is no point for me being on the helm.
Outside of these rare instances I am always on the helm as captain.