For each box, select all the marbles and the box and use Edit->group.
Then, when you are in group select mode, the box and it's marbles will move together. Switch to object mode if you want to move or work on an individual box or marble.
If you want to put these small boxes inside another large box, group the box with all the smaller boxes.
Use edit->ungroup to break down the groups.
Tools->hierarchy will be a help to visualize how stuff is grouped.
Andy
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