In MainStage, try to program as much modulation via the mod wheel into the mod matrix of a plugin. This is the best way to change multiple parameters of a sound with the mod wheel.
You could also use the MIDI Modifier to control volume, and then use the MIDI Input tab to send the mod wheel data to the plugin as well (just make sure the “thru” option of the Modifier effect is enabled).
Unfortunately, when you add a traditional “mapping” to the mod wheel (say if you wanted to have the mod wheel mapped to the bypass feature of the chord trigger), it stops the MIDI CC 1 (modulation) data from passing thru into the channel strips. Thus, if you want to use the mod wheel for mappings, you will want to achieve all of the effects via mappings rather than by using the Modifier effect, MIDI Input tab, or Mod Matrix.
For any type of off/on functions, you will want to use the “steps” option in the scale parameter area. Then you will be able to set your output cause via the MIDI data range of the mod wheel.
By using traditional mappings, you can just click the option that you want to map the mod wheel to (and then use the scale parameter option to tune in that mapping to a specific mod wheel range.)
With that said, we still prefer to use the MIDI CC 1 modulation data to control our song specific patches, and so we don’t make any traditional mappings to the mod wheel.