Usually, the size of the flint is dictated by the lock size. Most of the larger locks require a flint of at least 3/4 inch. 5/8ths flints are normally used on those dinky Traditions locks or on the small handgun locks. Larger flint such as 7/8ths and up are used on the big locks such as on a Brown Bess, etc. I've got 3/4x3/4 flints on my two kit guns, although the Queen Anne lock on my .62 cal smooth bore could probably benefit from a 7/8ths sized flint, as the lock is pretty big. I may try them.
As to bevel up or down, try this. Mount the flint in the jaws of the cock, then lower the cock into the pan as if the gun's just been fired. Take note of where the edge of the flint pointing. In other words, lay the gun with the lock facing up, and look at the touch hole. The edge of the flint should be almost right in line with the touch hole. If its off, you'll notice, then turn the flint over and try again. You're trying to get the shower of sparks to fall as close to the center where the touch hole is, if I'm explaining this right. This helps with ignition timing and to get the most out of the spark/priming charge.