Liz,
Any of the ways you suggested would work!
For my son this year, I placed the printed maps in a 3 ring binder with the Teacher Map first and the Student Map following it. That way the map my son needed to refer to was right before the Student Map he needed for doing his work. If you have more than one child who will be using the maps eventually, it may not be a bad idea to laminate the Teacher Maps, however it certainly wouldn't be necessary.
After the child finishes the Student Map, we file it in our History Student Notebook within the same unit that we are working on for that week. In that way, the map is right within the notebook at the time period in which we were reading about it. We place the completed Student Maps in plastic page protectors in our History Student Notebook.
One additional tip that I did find helpful was to write a page number from the Table of Contents of the Map Trek on each map (although this was something not included on my original version I received and I can't remember if page numbers are included on the version we had made for HOD or not). Anyway, if the page numbers are not included, this is a good idea as it helps my child find the maps much more quickly.
My son has loved the mapping this year, and the maps really turn out to be beautiful and colorful. There is so much information on them and they really help cement where things were happening in the world. We pray you will enjoy the mapping within RTR as much as we are!
Blessings,
Carrie