There is no hard and fast rule...
but it is best to determine which works best in your lock - and with individual flints, which vary somewhat in geometry and dimension.
I like to orient the flint so that, with the cock in the half cock position, the flint is as close to the frizzen face as possible, but not touching, with the rear of the flint in firm contact with the frizzen screw: this allows the shortest possible fall (and shorter locktime), while keeping the flint off the frizzen face for safety and to avoid damaging the flint. The flint should also contact the frizzen with a slight downward angle, to produce good scraping action.
Having said all that, it is also good to arrange that the flint contacts the frizzen about 1/3 of the height of the frizzen from its top, to insure enough of the surface is scraped to produce enough sparks. Then, it is necessary to insure that in seating the flint in the cock, it does not strike the side of the barrel when the cock falls. Ideally, the flint should come to rest over the pan, and that the sparks should land on the priming.
All of these things are important, but you will have to determine the compromises which work for you in your lock and with your flints - and remember that, so long as you are getting good sparks, good ignition and good flint life, it doesn't matter which side of the flint is up.
Keep your powder dry, and good shooting!
PRD1 - mhb - Mike