Go into Window_Message.
The look for the line:-
super(110, 302, 480, 160)
That is x, y, width, height...also note you can't change the y placement just with this part of code, but the rest is editable. If you want to change y, keep looking down till you get here:-
case $game_system.message_position
when 0 # up
self.y = 16
when 1 # middle
self.y = 160
when 2 # down
self.y = 320
end
end
That sets placement for Up, Middle and Down when called upon using message placement.