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The French in later years used the formation Mixed Order, and had 1 company of light infantry,will these companys moved from the reg. to skirmish in front. As far as ships go the BRIT 2ND Rates were of 2 types one with 18pdr and 12 pdr guns the other with both mid and upper decks with 18pdr will thses be shown as dif ships and or broadsides.
I doubt the ground battles will have any resemblance of this beyond a special ability (or two separate infantry units which you can then muck about with the formations like all other TW games) but the ships might have some sort of formation change depending on where the target ship is in relation to it.
As for whether two different ships of same type (e.g., second rate) would have different armament...unlikely. They'd surely be classed as 2 different ship types if that happens at all.