Thanks for playing:D I just made a small gameplay/hint video on this game and it contains the solution to the levels! It is at the bottom at the game page.
The three boxes level is definitely a challenge level I tried to design since I want to keep my gameplay short overall for Trijam. It required some repositioning for the boxes and utilizes the slow zone(In hindsight I should make something to signal that dark blue slows down the box).