[Supperman]

重なっている部分＝the crossover part where plural (2 or maybe 4) parts or origami paper are lapping over.
はがすようにして=like a manner of peeling off
まとめなおす=re-arrange

Please peel off the crossover part and re-arrange it.


Does it make sense in this case?
I'm not sure what it means.
Even native-Japanese couldn't understand what it means, without illustration.
Written description is difficult to understand, without illustration.

I wonder if you are making "orizuru"(paper crane).
If so, at the middle of process, the head, the tail, and the both wings are positioning together.(重なっている部分）
So you should separate the head part to the North direction, the tail part to the South direction, the right wing to the East, and the left wing to the West, making angles, and re-arranging it.