Sorry for the late reply. I had the same questions when I got mine programmed in, and that was 6+ years ago so bear with me.
IIRC, the bottom button was for remote trunk release if you had one (a trunk that is). Since we are talking about a taco/4Runenr there is no trunk, so the bottom button was essentially useless. You could program both top and bottom buttons to unlock or lock the doors so it would not matter what button you hit, you would get the same result.
There were no labels on those buttons.
There are instructions out there on the web on how to program the remotes. They are free, It involves a small, small screw driver/ or dental pick to push in the button below the driver seat, on the alarm module itself.
I cant remember the instructions off hand, but you push in the button under the seat, then push the button on the remote. and it blinks twice or something like that. and you need to have all the doors closed.
It was not hard and took about 10 minutes for both cars. and both remotes.
If I find the procedure I will post up a link.