So far, in my one moment of experience as a Captain, I've stuck to nautical terms when speaking about directions relative to the ship, but switched to left/right when explaining something to a specific crew member who I can see and know which direction I want them to go relative to their character model.
Unfortunately, in that one battle, I kept forgetting the game is push-to-talk, so my instructions were "ignored" by my crew. Then I got yelled at for not being a good Captain. I'm pretty sure that was a fair assessment of my performance up to that point.
As an Engineer, I've rarely found any need to give directions beyond "I'm busy with the Engines and Balloon, can someone get the Hull?" so looking beyond the edge of the ship is a rare occurence for me during combat.