Collection Plate
At the end of watching the video from solving Puzzle Box 2 you see at the end the words "/collectionplate". After going to http://vanishingpointgame.com/collectionplate it tells you when the time is right I will ask you a question, and also says _ out of 36 found. This refers to the White Boxes found in each puzzle. Since there are 36 boxes. That means there are 9 white boxes in each one puzzle box. After finding all 36 you return to http://vanishingpointgame.com/collectionplate and it will ask you a question that you must answer to win the meta puzzle.
Locations of the white boxes are shown below (more required):
Week 1 -
In progress (written out temporarily until someone uploads pictures)
Watch Springs Whitebox - on the bottom left between the letters T and W
Mantle Clock Whitebox - on the top right hand side of the submit button
Gears Whitebox - before the clock disappears and goes to the gears, it is located on the top left of the clock near the bar
Airport Whitebox - right next to the word D in Departure
Cuckoos Whitebox - in the empty clock at teh bottom on the bottom left
Starfield Whitebox - on the bottom right where the big house (mansion) is. Right on top of the the house
Calendars Whitebox - on the bottom left of the note beneath the number six (6)
Repair Table Whitebox - on the left side of the yellow clock
Hourglass Whitebox - next to the 12 second hourglass's right pillar. On the top right, beneath the curve
Week 2 -
The meaning of the white boxes, including clearer pictures of the boxes themselves, can be found at White_Box_Phenomenon