#1 - for the windows you can make a boolean Select the box ->Boolean->select " Subtract (B-A), then select operand button and click on the fuselage.  With any luck, you'll have the " windows" cut out.

#2 - Create a spline, shape it to the window form, and use the shape merge tool.  (click on the fuselage, compound objects->shape merge; select shape and click on the spline you just formed. 
This will trace the shape onto the fuselage.

Hi there Citation!

What a nice design uhn?

Is this F-102/106????

looks nice!

cya.

Go back to the earlier version from your first post above.

Use cut/refine option of boolean to cut each set of windows and doors, one set at a time.  Make sure you have Edges Turned On in the viewport so you can see your cut lines.

Once everything is cut, then you can detach all the windows and doors individually.

When you have everything detached and all the exterior model in a finished condition, then you can clone the fuselage, name it fuseinner or anything, and select all the polys and flip them.  You must be in editable mesh mode to do this.

Once the fuseinner is ready, hide everything but the fuse shell, then select all the fuse polys, go to extrude, check Local option, then extrude 2-4' inward to give the fuselage depth.  This eliminates the see-through issue and provides the interior shell.

Hope this helps.