How to align different parts together

I'm designing an odd looking cube-like object with 6 planes. You can imagine it is a hollow box that is form by 6 planes. Each plane is a polygon with 4 vertices. If each plane is created as a part each and then piece together in an assembly. These planes are not exact squares which hence doesn't fit into each other nicely

I am facing the problem that I can't align all the sides to be coincide with each other. 3 planes assembling together is easy, once I add in the 4th plane, I can't easily coincide planes together without creating an over-defined mate.

Can anyone here help me out on this ? Please advice.

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