Thanks very much for the suggestions.
It looks like I did not pose the question very clearly.
We desire that the surface displays something like "Hello[1] world[2]" on the VE surface and then have the footer note pick up these [1] and [2] automatically and display them for us at the bottom of the page as in the case where <ref>{{cite|a}}</ref> gets picked up in wikicode and rendered.
Is this possible?