Here's my method, which I warn you is crazy, but go with it:

- line up the saddle with the top tube as precisely as you can;
- line up the front wheel with the frame and hold it there (a friend is handy here!);
- follow the line of the saddle with your eye so that the stem, top tube and the line of the saddle are all on the same plane.

Told you it was a bit odd, but I guarantee it will work. Ish!