You will want to create a new folder dedicated to storing the updates for the new Deployment Package.
The distribution of third party patches is handled in the same way that first-party updates to windows and office are.
It should not be located in your WSUS folders, but instead in a similar location to your Microsoft Updates. Whatever source location share you are already using for other things such as updates, applications, etc.
Configuration Manager will download the updates from WSUS, even if it is on the same server, and then process the content and put it into the folder specified as the source for the Deployment Package.