Two concepts can form a new one.

I'm currently reading about the topic and looking for appearance.   First, I'll do a basic implementation — I'll probably use Greek or Hellenistic ships as the standard. For the first implementation, I'll only use the crew's controls. That's the thing I mentioned. Also, in theory, they should give bonuses to the ships. The boarding combat simulation will be important. It probably needs to render some troops as virtual, without a 3D graphical existence like their ground counterparts.   It would work like an inventory system in RPGs; if you change something, it will change the ship's stats.

As with everything, I strongly advise to consult the available information. Greek ship crews are well attested, for an Athenian triḗrēs for example: "the specialist assistants to the trierarch" are "the ὑπηρεσία" (hypēresía), which "in the strict sense was composed, in threes, of 30 men: the helmsman (κυβερνήτης) with an aft deck-gang of 5, the bow officer (πρωράτης πρωρεύς) with a forward deck gang of 5, the rowing master (κελευστής), the purser (πεντηκόντάρχoς), shipwright (ναυπηγός) and the piper (αὐλητής). In addition there were ten hoplites and four archers. These, with the 170 oarsmen made up the three's crew of 200" (201 including the trierarch, apparently), from Greek and Roman Oared Warships, 399-30 B.C., by J. S. Morrison. He then describes the crew of a Rhodian tetrḗrēs, and so on. This whole book is a necessary read on the subject.

I'm creating some mock-ups Here I am placing the commander.

Gatehouses. I believe that mechanic exists in games like Stronghold and Caesar III. They can even function directionally. If they're oriented one way, it's input, and if they're oriented another way, it's output.