First I would just like to say that your map look very nice and interesting.
However, the bonus boxes being on the side is very annoying during gameplay, especially when the bonuses are not clearly defined. You have to zoom in and out at each move to see where you need to go. This has proven to be a defining thing in some good maps being ignored and not played. The megabonuses and the other special bonuses can be placed at the side.
I strongly recommend that you place each box in their respective bonus. Contrary to your belief there is ample room for them. Just an example.
But in the end it's your map and your decision is of course final.
Good luck with the map :D and i hope you continue making more of them :D