The way I do it is to make a template out of thin mdf then use that to route a thicker template with a top bearing flush bit. Then I use the thick template to flush route the body. Depending on the length of bit and depth of plunge, work your way down. If you can't do that, flip the body over and use a bottom bearing flush bit, using the bit you've already routed as a guide. Always work with the cut - anti-clockwise on external cuts, clockwise on internal cuts like for the pickups.
A lot of people will cut the neck tenon first and then make a template to fit for the neck socket in the body.
I assume you are competent with a router?
Guide bushes are more useful for smaller internal routes such as pickups, although a lot of people just flush route to avoid having to work out and accurately draw the offset. However the guide bush means you can use a thinner template.
It's always useful to do a test route on scrap wood to check you've got the template right.