Well, I suspect that there is a better way to do whatever it is you are trying to do by checking those values.
However, you can check if an event is through by placing the following code into the script field of the conditional branch:
$game_map.events[event_id].through
where event_id is an integer corresponding to the ID assigned to the event you are checking.
always_on_top is not, by default, publically accessible, so you will need to first insert a new slot in your scripts, and in that, paste the following:
class Game_Character
attr_reader :always_on_top
end
Then, in the script field of the conditional branch, check the following:
$game_map.events[event_id].always_on_top
where again, you replace event_id with the integer ID for the event you are checking.
If you want to check either of those values for the player, then the code is:
$game_player.through
$game_player.always_on_top