Welcome Aboard!

Go to the Ship Equipment (SE) screen (press 'e' ). A blue hand in the lower right corner of the icon shows which ship and/or equipment is equipped. If there is no blue hand, then that ship or piece of equipment is not equipped.

Things to know: First, ships and equipment are by maker (Pirate, Monquistan, Bison, etc.), size (Raft, Skiff, Frigate, Galleon, etc.), and type (Rudder, Cannon, Anchor, Armor, Horn, Figurehead, Sail, and Wheel). Most ships of one type and style will NOT be able to use equipment for ships of another type and style. The type and style of a ship or piece of equipment can be seen when you hover the cursor over the icon. There can be only one type of equipment equipped at one time. There are at least 2 other restrictions: Level (LVL) restrictions (what LVL your character is at) and Nautical Level (NL) restrictions (what NL your character is at). Both levels can be seen on the Character screen (press 'c'). The LVL or NL restrictions, if they are there, will be shown when you hover the cursor over the icon.
There is no restriction if it is not listed. Selecting or de-selecting is done by double left clicking on the icon or click on icon and then click on the hand in the same screen. A lock on a piece of equipment means it cannot be used on the selected ship.

Select the Raft. Then remove all items from it. Select the Skiff and select all the equipment that does not have a lock on it. You will notice as you equip items that their icon appears next to the ship. The missing equipment must either be bought (using Gold or Crowns) or acquired as loot. I recommend at the very least having a Wheel (repair), Cannon and Figurehead (attack), and Sails on a ship.

Hope this helps. Good Luck!

Ship parts go by type of ship too. Your raft can only use raft items. The parents Skiff with pirate type origin can only use Skiff items with the same origin. Check the shop at Jonah Town docks for the correct ship parts. One thing to keep in mind that some ship parts require a certain Nautical level. You Nautical level by defeating ship battles.