Mainstage has access to all the effects and instrument plugins of Logic !
So, any MIDI Input device (keyboard, guitar, controller) that sends MIDI note events can control any of the synths, samplers, drum machines, organs, electric pianos, etc that are available in Mainstage.
Additionally, you can place any effect plugin on these "software instrument" channels. e.g. delays, reverbs, compressors, filters, EQ, stereo wideners, guitar amp simulators, pedal board, wah, flanger, the list is too numerous to mention here..
Yes, you can control any Software instrument, like Arturia MiniMoog or Atmosphere, Omnisphere, RMX, Konakt, etc which is compatible with the Mac OS version you are running and in the 'Audio Unit' plugin format.
If you are using an Intel Mac then Atmosphere may cause you some problems as it is not natively compatible with intel Mac architecture. Check out the upgrade to Omnisphere. It contains all the original atmosphere sounds and much, much more!
Hope that helps