The Workbench upgrade should not affect anything you can do with the JTV in your Vetta, or X3. The Vetta/X3 capabilities apply to the JTV itself, not Workbench. The JTV v2.0 firmware update affects the modeling that the JTV uses but, again, that should not affect anything to do with what is stored re: JTV presets in your Vetta/X3. Anything you could do before you should still be able to do. Remember, the Vetta just stores JTV settings - it has nothing to do with producing the JTV sounds.
Note that the Vetta/X3 are limited in what they can do with JTV presets compared to a Pod HD (e.g. can't store JTV alternate tunings in a Vetta/X3 preset, but can in a Pod HD500 preset) but that has always been the case. The JTV/Workbench updates should be transparent to you as far as your Vetta goes. You will, of course, hear the new modeling in your JTV.