Didn't read the other replies.
The yokes on the UJ's have to work in unison. By that I mean if one of the UJ's bends toward you, without moving anything but the other end, it MUST move toward you too.
To effect this safety feature, most drive shafts are keyed such that you can't assemble it unless you get the two lined up as mentioned.
On which is which, it doesn't matter per se. But, if you put the larger shaft end below (on the mower) with the smaller end on the tractor and leave it in the weather, especially with no safety shields, the mower end will fill with water and eventually freeze up your slip joint and that, carried to the limit, can gut your pto from your tractor, the first time you go over a hill or gulley, depending.