If you make your own template, nail or screw a 1/8" (or a little more) over-hanging spacer on top of your template. Fit it over the door and route your hinges. When you position the template into a new jamb, the 1/8" spacer will provide clearence for the door crack at the top and locate the hinges opposite the door hinges. If you are using old jambs, you could match your template to the jamb hinge spaces using your 1/8" spacer. There should be enough paint and crude around the old hinge spaces, that a fresh router cut would just clean it up.

Chuck