To be candid, the first step in this process is to thoroughly research the requirements for implementing Configuration Manager, the effort that will be required to build out that implementation, and the significant differences in the update management process between WSUS (native) and Configuration Manager.
If you choose to implement the Configuration Manager Software Updates mechanisms, then you will have some minor changes to be made in the Extension Pack. Once the Configuration Manager environment is implemented and operational, the Extension Pack changes are relatively trivial.
1. Register your Site Server(s) with the Extension Pack.
2. Register your Software Update Point with the Extension Pack.
3. Publish updates to the Software Update Point, which is done in exactly the same manner as you have been publishing to your WSUS (native) server.
If you choose to continue doing update management with the WSUS (native) environment, not with Configuration Manager, then there are no changes required.
You cannot use the 3rd Party Updates Pack without the Extension Pack. The Extension Pack provides the infrastructure necessary to make use of the 3rd Party Updates Pack.