The cabin is made with extrusions, as was the boat. By copying faces from the hull as the basis for the cabin, you will make sure that the cabin will fit snugly on the hull. Execute the following steps:
Press Z to toggle Viewport Shading to Wireframe.
Press the Tab key to go into Edit Mode.
Press Shift + D, and then press Enter to copy the cockpit floor. Press P to separate the duplicated faces. Choose Selection, as seen in the following screenshot:
Press 3 on the NumPad to return to the Right view.
Press the Tab key to go into Object Mode. With the RMB, select the copy of the cockpit floor that you have just made.
Press M, 2, and then press Enter to move it to layer 2.
Press 2 to go to layer 2, or use the Layers controls in the 3D View header.
Press 7 on the NumPad to get the Top view. Press the Tab key to get into Edit Mode.
Press A to deselect all faces, if needed.
Press B and use the mouse to select the faces that are in the cockpit area and not in the cabin...