The question as it stands would require a book to answer it. Luckily for you, the book has been written: "Naval Warfare Under Oars, 4th to 16th Century" by Rodgers (1940). To quote from Chapter 8 on the Italian Naval Wars in the 13th century:
Ordinarily, squadrons moved in column with the admiral leading; in
battle the fleet formed in line, sometimes in a straight line,
sometimes a crescent with the wing ships either advanced or
withdrawn.... Frequently, when the fleet was near the shore, the ships
were bridled for battle; that is, they stretched cables from one ship
to the next, so that the enemy could not break through the line....
The engagement commenced at a distance with flights of arrows, stones,
and bolts from the machines. When attacking sailing ships, it was an
object to tear the sails with arrows and cut the rigging with scythes.
After ships collided, the rowers left their oars to fight; divers
tried to bore holes under the water. Liquid soap was thrown on the
hostile decks to make them slippery. Greek fire was thrown in pots and
also quick lime, liquid pitch, and boiling oil and incendiary
darts.... It is noteworthy that few ships were sunk by the ram or
otherwise as compared with ancient times. For siege work the ships
rigged flying bridges and ladders from the masts to swing against the
walls and enable the soldiers to reach their tops. On the other hand,
the entrances to harbors were defended by chains drawn across the
channel, and on some occasions by piling (lizze) driven to obstruct
the channel and by sunken ships.
To answer your question more fully you may want to get this 350-page book, published by the United States Naval Institute Press.