HW, love the user name!
I can't post links/images yet, so I'll just try to explain this as succinctly as possible, and probably fail miserably. Wish me luck. I'll go into a good bit of detail, you very possibly know much of this already. Sorry if I'm repeating old news lol.
I'll assuming you're referencing a strat or tele neck and pocket, if it's something else, like an ibanez with either a square heel or the newer AANJ, or maybe a set neck like an LP, let me know.
The heel is basically a rectangle, on a strat the edge that faces the body is curved out a bit, and on a tele it's flat. On the other end, the rectangle basically ends and it starts tapering in to the curve of the neck. Usually, the neck pocket ends ~1cm or so from where this taper starts. align this imaginary edge of the neck over some MDF, and trace it out. Make some marks where the last fret is, you'll need those to measure out how deep to set the pocket. Don't just trust the end of the body on that one, it may be too far out if the bridge is already routed. Go ahead and cut out the neck pocket on the template, and a square around it. Enough room to clamp it to the body, and to see the marks for the fret.
Now take note of the distance between the front of the nut where it butts up against the fretboard, and the center of the last fret. Similarly, measure the nut to the 12th fret, and double that. That distance away from the nut is where you want the intonation point to be when your saddles are moved all the way forward (or just a hair in front of your high e, if they dont move). Take the difference between the long length (aka your scale length) and the last fret to the nut, and thats how far you need the marks we made to be from that intonation point on your bridge. Using that number, you can clamp that template onto the body. If the body is already cut out, odds are this lines up nicely with the spot for the neck pocket already, but I like to measure twice (or maybe 7 times or so) and cut once.