In the cleanup phase, should all the research tiles be removed from the supply board before new ones are drawn from the bag, or does the amount of research tiles available grow if there's still tiles left? If so, if you draw tiles that's already on the board, do you just stack them on top of eachother?"Draw new Technology Tiles (according to the number of players) from the bag and place them on their respective places on the Supply Board." (English rulebook, p. 24) Do not remove tiles already on the board (because the rulebook doesn't say you should).
Much like initial game setup (English rulebook p.5), duplicate tiles of the same technology should be stacked on top of each other