In Motion, when you apply the filter to footage it should show the Onscreen Controls. If you select another object the onscreen controls for the filter will disappear. To see them again, select the filter in either the layer list or the timeline.
If you've made a Final Cut Effect for the FxPlug, then you need to check the "Publish OSC" button at the bottom of the list of parameters. Once you do that, if you apply the effect in Final Cut, you should see the onscreen controls. If not, make sure the piece of footage the effect is applied to is selected in the timeline, and then in the inspector, also select the effect.