Merely place the document in a sheet protector, with an acid-free page of paper to separate it from the reverse side document. As for filing the documents in an understandable order, we suggest a numbering system. As each document is received, it is put in the next page protector and given the next available number. Notation of that number is made on ALL family group sheets it documents. As notebooks become full, another is added.
Some people suggest keeping all like documents in a single notebook.
This involves using more notebooks, but then all the census records would be found in one notebook separate from the birth records notebook or the marriage records notebook, etc. Although much has been written giving suggestions for organizing your documentation, it ultimately remains your choice. After all, it is YOUR family history. Please remember that others need to readily identify your method of organization. Without documentation, the family history is reduced to nothing but hearsay evidence.