and check the effect by activating the controls on Beatstep
What do you mean by this? Do you mean that you are 'learning' control when you have both open? There's no need to do that.
Restore the default beatstep setting to your computer, rename as hammond then store it on your beatstep - Close MCC
Open your VST, go into learn mode and move the controls you want control for. Either save or come out of the DAW midi learn mode and you should have control. You can now store that setting on any pad you like.
Or if you need different control options, rather than editing the same patch - Save a new one. Duplicate that same preset onto your computer, save onto another pad on your beatstep and change the midi CC for the control you need to alter. Then re-learn that new CC and you have 2 presets.
There is no need to have the MCC open at the same time. If you know the Midi CC numbers you need to edit, just input them, if you don't, you save a default pad and let the software learn the controls.
Hope that helps