It does make it a little harder with two teams, but it can also make it easier. If you are building formations to accomplish one particular thing and you build playbooks to accomplish one particular thing, then you can share those settings between teams, and if you adjust the playbook it should be valid for both teams within the context of what that playbook is for. If on the other hand you set one playbook you have in mind for your Main playbook and you plan on adjusting that for your opponent, then yes you are going to need one Main playbook for each team.
My plan is to add a helper tool on the side that lists which playbooks you are using (have in your game plan) for all of your teams. If you do want to keep certain playbooks team specific, you can't filter them right now, but you can name them, so I would prefix them with something that you can identify them with and if you use the prefix it will help in sorting them on the playbook page so they are grouped together.