There's one major problem with the MIDI control mode: upon reentering Spark Mode, one must reconnect to Spark, there is no other way than clicking on the 'reconnect' button in the Spark plugin/standalone window.
That said, simply open up the MIDI control app and set whatever midi message you'd like to send for whichever control on the spark.
How you prefer to do this is going to depend on your unique setup. There are no hard and fast rules other than KISS: keep it simple, stupid. Best practice usually to map to the controller not the controllee.
IMHO, until the Controller can reconnect to Spark on its own, it completely defeats the purpose of of a controller: to remove the user from needing the mouse.