Have you read, the similarly named, Galleons and Galleys by John F. Guilmartin? He covers the development in the time span you are looking at.
Galleys mounted a heavy centerline cannon from an early point, usually much heavier than what you would find on a sailing vessel, and they did on occasion sink sailing warships outright with them. Any cannons in the stern would have been very light, usually swivel guns, although possibly something a little bit heavier. Galleys attacked with the front, and it sounds like your rules already take this into account.
When sailing vessels started to carry heavy guns, they often placed them in the back on either side of the rudder. This was for purposes of stability, but also provided a defensive measure if being chased by a galley. This part of the ship became known as the gun room, and often the heaviest cannons would be the stern chasers. As ship design developed more cannons could be carried broadside.
It should be remembered that broadside tactics weren't really developed until the Anglo-Dutch Wars (although there were a few antecedents). The forecastle was the offensive part of the ship, and there were some attempts to improve forward firing artillery. This was always limited on a carrack, with it's high forecastle, but the galleon allowed heavier guns to be placed there. If making an artillery attack (as opposed to trying to force a boarding fight), the standard tactic was to close and fire all the guns on one side of the ship, turning to show other sides of the ship until all the guns had been fired, then pull away to reload. That way both broadsides, bow chasers, and stern chasers were fired at the enemy (I forget the precise order). English galleon captains appear to have felt that the bow guns provided the "knock-out" blow.
I guess the answer is it depends upon the type of ship. A very early 16th century carrack may have only have had stern-chasers. And, as GlidasFacit pointed out, on most sailing ships the stern chasers would be more powerful than the bow-chasers.