do ships count towards the number of units you have on the board

Ships seems to confuse the rules for us.

Thanks

Yes they are also have to be in your supply limit and also you can destroy a ship if wildings win in wildings atack session.

There is no reason why this should cause confusion. Simply understand that all wooden pieces on the board count towards your supply limit. That includes infantry, knights, ships, and if you play with the respective expansion, siege engines.