I would guess something more like a Coston Light would be easier to transport, and safer while sitting in a small open hatch, low in the water, of something like the Hunley. It also would give the user a preset coded signal to indicate to Battery Marshall. Signal-pistols did exist that fired the Coston Light system and the Confederates in Charleston used Coston Lights.

http://www.civilwarsignals.org/pages/signal/signalpages/flare/coston2.html

David