You need to make sure you setup your I/O Setup.
It should look like this when done.
Im running the 002 rack on a mac with an MPC 2000, Emu Proteus and Mophatt, And a roland mc-303.
Once you have setup ur I/O setup, you can now assign inputs to new audio tracks in you session. (see blue circles) Once you have selected the input you wanted for that track click the record button in that track, that will allow you to listen to the input before recording. After you have recorded your track unclick the record button. (see Red circles)
I made a session file with all my inputs assigned, i use this while producing. once im ready to record i make a new session with the inputs i will need.