I used a similar cheap version to what you probably just bought on amazon. Just tighten the handles down well and go slow. They aren't perfect but they are a heck of a lot better than trying to free hand it.
Like watermann, I also put the new transom in the boat, marked the holes, removed, and then drilled. I did all the holes except the splashwell drain tube holes before putting spar varnish on the transom. I decided to hold off on the splashwell drain tubes because I wasn't certain that they would line up perfectly with the bottom of the splashwell on the interior side by just drilling them 90 degrees, and I was so glad I waited. They ended up needing to slope upwards somewhat in order to land in the right place. I hope that makes sense. Your boat may vary.