The electronic controller goes on the opposite side of the bike to the vacuum controller. If you already have the original CC the electronic controller's cable should just pop into the link-case (unless they updated the link-case' as well).
From my experience with the V-Strom electronic CC, you gain a much more precise operation of the throttle. Plus, of course, you don't run the risk of pinching the vacuum line, which was the bane of my existence on Ruby. Somehow the route it took made it vulnerable to being pinched, especially by the seat.