Ok worked it out. You just need to create a "New Link" for each source. So, for example, say you have your automation already assigned to adjust filter cut off, it will be listed under Internal Controller - Automation Clips. Now you need to click on New Link, then just move the knob on your control surface. It should pick it up, now you will have 2 links for the Filter cut off.
Spent WAAAAY too long trying to work out something so simple.