Without knowing exactly what your set-up is, it's a bit tricky to advise - but in theory this should be possible.
Press the 'i' in the top left of MainStage and click on the channel strip with Equator. You will now see the Instrument Channel Strip Inspector along the bottom. In the 'Layer Editor' you can specify a key range for the Seaboard Block that isn't playable by your other MIDI keyboards; like C7 to G8 for example. In Equator's 'Global' and 'Preset Master' tab, you can transpose ±3 octaves to get back in the correct range.
I hope this helps!