This is a pretty easy step. It takes the Booleans you have made and converts the Boolean operations to a mesh model, just as you converted the Subdivision Surface to a mesh model. Check the following steps:
Select Cabin. In the top Add Modifier subpanel, click on the Apply button. This will make the Boolean modification permanent.
Now, repeat this for the other two Add Modifier subpanels.
In the Layers buttons of the 3D View header, select Layer 1 and Layer 2.
Use the MMB to inspect your sloop.
Increment the filename and save the file.
Congratulations, the sloop is well on its way. You have completed making the hull and the cabin. Making the basic shape of the cabin was very similar to how you made the jon boat. The big change was using Boolean modifiers. They made quick work out of cutting out the portals and the door.
So, with your model, the Difference operation left the entire cabin that was not part of the Door Boolean and...