Stratagems permission work a bit differently that the rest of IPS.
The goal of the permissions are to create a team and assign them appropriate permission regardless of group.
When you first create a project, the only user who has any permissions would be the creator/owner of the project. they have all permissions, that can't be revoked or restricted in any fashion. The owner can then proceed to edit the project and add members/groups to the Team on the team tab. Here you will be able to give them permissions thru out the project. they each have descriptions, if you have any questions or want more detail on what a specific permission does, feel free to create a new support request.