Another vote for Hiscock's book - he builds three different instrument showing the three styles of neck attachments (set or glued in, bolt on and thru neck) on both flat topped (Fender style) and carved top (Gibson style) bodies. He talks about all of the geometry issues as well as tools, materials, finishing and wiring. I built my Les Paul copy using only that book and a good set of plans.
Tell us more about the instrument you want to build - are you using plans and if so which ones? There are some very good build threads for different kinds of guitars - those can be very helpful.
And yes, the total thickness is whatever is called out on your plans. Often the body is hollowed out to remove some weight and/or to provide channels for wiring. Top plate is usually a fancy piece of wood that covers the channels and of course looks good. Here is my Lester - it is flamed maple over a mahogany body
One thing to think about if you are going to use a cap is whether you will put a binding on it - the binding frequently will cover the glue seam so the thickness of the cap should be less than the height of the binding. Hiscock explains all of this and you can see the binding around the edge in the picture.
?adma