We are developing tooling to help with the migration from V2 to V3 now. It is expected to be available in December. The tooling will ensure devices and users can move to V3 easily. However, configurations like CDE, Dashboards, Rules, Jobs and Groups will need to be reconfigured. (They are just too different to migrate automatically).
Without this tooling, it is possible to migrate now, but you would need to create a new V3 app and then update the device scope ID on your devices to use the scope ID for your new application. (Using the migration tooling will not require updating the devices)