This will be unlocked through Natural gameplay I presume. As previous assassins creed games you will get to a point where you are forced to upgrade the ship to carry on tgghe storyline.
Ways of getting resources -
Looting dead corspes
Buying from Merchants
Spending your Helix Credits on the Time savers packages
War Supplies. Make sure to LOOT them before burning (good source of resources)
unlocks at 29:50