How to I “set out” the holes for hinges?
If you're going to recess the hinges, you'll want to create a jig and use a router for the recess. I would recommend aligning the door and frame together and marking between the two at each hinge location as a reference point so that you don't install one at the wrong height.

When you're ready to screw in the hinge, place it on the door and frame to mark the locations of the screw holes and then drill pilot holes. Make sure your drill is level and square to the surface so you don't end up with crooked screws.

Finally, when you first attach the hinge to one side, don't tighten it all the way down, leave some play in it. Do the same when you screw it in to the other surface. Then tighten one screw on each side at a time, verifying that the door still swings freely as you go.