Michael - a couple of us have a secret to how to do both sides of a guitar at once - grab a hunk 'o wood - thick enough to take the weight of a guitar. Slot it into the neck pocket - may need to tailor the wood to do so. Drill a couple o' holes through the wood via the screw holes (spacing is pretty much constant between guitars and basses). The secret sauce is then screws and wingnuts to hold the guitar on. Screw head on the back of the guitar and wingnut on the other side - this way when you're done, it's easy to get it off the stick. I have a painting stick that I rest one end on the ground and then use some quick grips to hold it onto the edge of my benchtop. Others drill a hole in the other end and then suspend from the ceiling / roof / whatever. Comes down to what works for you. Given that the body is not resting on anything - you can work on both sides at once.

When you have a set neck - easy solved - I find a well placed quickgrip with some wire and suspend from the roof / ceiling / whatever. Gives you a handle for the guitar as well.