Sure! You load it in the instrument rack, and then select it as MIDI input in any MIDI or instrument track you'd like to control. For MIDI control of thesys itself, make a MIDI track and select it as output.
This is really a hot discussion in this forum ... I hope that it is not too sleepy for somone to find that post:
And the question is: would it be possible to run different sequences at one time in parallel with one instance of TheSys, e.g. have different loops independently from on another. with different length and velocities ... ?