For seat, I align my eye (use only 1) so the top and down tubes are aligned with one another perfectly. BB shell can be useful if the downtube isn't larger than the toptube. Now, the nose of the saddle should be centered on the toptube, without moving bike or head.
For the front end, again align your eye with top and down tubes. Ensure front wheel is aligned with top/down tubes by judging tread visible on each side. Ensure stem bar bolt is centered on tire's tread pattern, again, without moving bike or head.
Just like siting a rifle.
J