GoPro Studio 2.0 and CineForm Studio Software has an auto-pairing feature which will determine whether a match for 3D is available based on many different aspects of data. If your clips do not have the same name the system will still attempt to auto-pair your file. In some cases you may find that it has not. If this happens you can manually pair your mislabeled videos using the Manual Import feature in the import queue.
Note: it is always important to organize your media before beginning a project. If you find that your clips are out of order, or scattered, it is always a good idea to organize them before you begin importing them into the software.
Please watch the below tutorial on importing clips into GoPro CineForm Studio: