Hi John,
Making guitars (I presume electric) is a challenge for a newbie. But once understood is relatively easy.
1) spoilboard - no need to worry about that because I think you will be supporting the billet in air
2) For setting the tool I use a pointed tool or the actual tool. Once set it does not matter unless you crash or stop the machine somewhere through the program
3) use fusion for the geometry and the toolpath
4) because you have to turn your billet over I expect you will have "tabs" (say 3 or 4 ) around the guitar with holes in the tab. These holes will be used to hold the part and when you turn it over register the part for the other side. Once done these are cut off and their surface sanded. You need to make a "sub-board" or a bolster that can be screwed into that is held to the base board. There are other methods but this will work for you. If you search for guitar making videos there's lots on the web... Peter
other methods are using vacuum clamps or clamps that are used and removed and replaced as the tool moves around. These are complex for a learner.