It will be easier to help you if you supply sample documents.
You may have as many unwind stage as you have array in your documents. Example:
// Starting with the following collection with 2 arrays
c.find()
{ _id: 1, a: [ 1, 2, 3 ], b: [ 4, 5, 6 ] }
// A pipeline with 2 unwind stages
c.aggregate( [ { '$unwind': '$a' } , { '$unwind': '$b' } ] )
// Gives the following
{ _id: 1, a: 1, b: 4 }
{ _id: 1, a: 1, b: 5 }
{ _id: 1, a: 1, b: 6 }
{ _id: 1, a: 2, b: 4 }
{ _id: 1, a: 2, b: 5 }
{ _id: 1, a: 2, b: 6 }
{ _id: 1, a: 3, b: 4 }
{ _id: 1, a: 3, b: 5 }
{ _id: 1, a: 3, b: 6 }