I'm not the expert on sprouting pecan trees, but the $#%@^^$ squirrels that I share this bit of the Georgia pine woods sure are. They have them coming up all over my garden. When I dig hugelbeds, I can count on hitting a few nuts in the process of germinating as you describe.
As long as they are early in the germination process, I think you can just put them where you would like the tree to eventually be and not run over them too many times with the
lawn mower. The first thing the seedling does is to send down a taproot and get it well established, that's why little 6" twigs of pecan tree keep coming back again and again, like bad Mexican food. About the only way you can keep it from coming back is to get a good grip on the seedling and yank out the whole taproot, usually after a heavy rain.
Good luck! (Even though you really don't need any)