It is possible to make discrete multi-track impulse responses—even if you don’t have enough speakers or microphones. As you will only be recording one sine sweep at a time, you can set up as many speakers as you have, record them into Impulse Response Utility, then move the speakers to new positions, and repeat the process. To give you an example, imagine you only have a stereo pair of speakers, but want to create a quadraphonic impulse response, which requires the recording of four tracks in four different speaker positions. You could set up your pair of monitors, record their output, then move them to record the other pair of tracks in the other two speaker positions.
This method of creating impulse responses is obviously more time-consuming, and not having all your speakers set up at once makes optimal monitor placement—relative to each other—difficult. With time and careful planning, however, you can still achieve the same results.
You can also create multi-channel impulse responses in Impulse Response Utility through use of the Mono to Omni Discrete impulse response format. This only requires the recording of one speaker by as many “channel” microphones as needed (for the chosen format). The resulting impulse response places a lower strain on your CPU. See Recording a Mono to Omni 5 Channel Impulse Response.
If you have enough monitors, but not enough microphones, you can set up the required speakers, and move your available microphones between them. This makes optimal microphone placement—relative to other microphones—difficult, but you still have the advantage of optimal speaker placement (and it’s considerably easier to move microphones than speakers).
If your audio interface doesn’t have enough inputs and outputs—for the number of speakers and microphones you are using to create your impulse response—you can still set up all mics and speakers. As you record different tracks into Impulse Response Utility, you will need to disconnect/reconnect the speakers and microphones, in turn.
A more detailed discussion of speakers and microphones that are suitable for creating impulse responses, as well as suggestions on speaker and microphone placement, is found in Speaker and Microphone Selection Suggestions and Speaker and Microphone Placement Suggestions.