If you check seats with your luggage, they will be handled by the automated belt system and they land where they land; they are stacked onto the carts as they come off the belts. They will not honor any "fragile" markings or anything like that; if you want that kind of handling you have to ship them as a cargo package, which would mean that you would not have a choice as to which plane that they got on. It's not that they put them on the bottom on purpose, you understand, it's just that they don't have time to rearrange things to make sure they are on top.
If you take the seats to your gate and gate-check them, then they will be placed into the hold of the plane last, after all the checked luggage has been loaded, and they will only be placed on one belt (the ramp from the jetway door down to the tarmac.)
Aside from the issue of the weight of the luggage, I gate-check because I don't like risking that the seats might be mis-routed in the bag room and end up on a different flight. We can't leave the airport without them, after all.