When using Plug-ins with FL Studio, only the keys that may be operating as CCs are usually filtered.
In all cases, first make sure that in standalone mode everything runs just fine and that all the knobs and faders are serviceable.
Make sure to refer to the steps below to map your controls:
1. First click on the "MultiLink to Controller" button located on top of the FL Studio interface.
2. Move the plug-in parameter you'd like to map to your control with your mouse.
3. Now, turn a knob or fader on your controller and you should now have the control properly mapped on the desired parameter.
4. Repeat the same operation for all controls.