I was watching some streamers play Blackwake, an Age of Sail naval combat game earlier today, and noticed that people stationed below deck had difficulty discerning which side to go to when, for example, they heard an order to man the cannon on port side.
In the past, were the interior of ships marked so the crew could quickly easily find which side was being referred to?
Shameless /r/BlackwakeGame plug
Not really no, at least not in any source I have seen.
Simply because once a new seaman had a rudimentary amount of knowledge it wasnt often something you would mess up.
The reason for this is that Port and Starboard are not relative to your position when speaking, they are fixed relative to the vessel. Starboard is ALWAYS going to the right side when facing the bow of the vessel.
So as long as you know where the bow is you know which side is which.