Any two Ensemble Thunderbolts (or an Ensemble Thunderbolt and any Element Series interface) can be connected in Multi-Unit mode.
First, make sure to download and install the drivers for Ensemble and Element.
Then connect each unit one at a time with a thunderbolt cable to your Mac and run the Apogee Firmware Updater app in your mac's Utility folder to update your current firmware on each unit.
Then to connect in Multi-Unit mode:
1) Use a Thunderbolt cable to connect any Thunderbolt port on Ensemble directly to a Mac's Thunderbolt 1, Thunderbolt 2, or Thunderbolt 3 port.
2) Using a second Thunderbolt cable, connect from Ensemble's 2nd Thunderbolt port > to the thunderbolt port on your Element Series interface (or second Ensemble).
3) Using Optical (Toslink) cables connect from the 1st Unit's ADAT Optical OUT Port 1 > the 2nd Unit's ADAT Optical IN Port 1.
Do the same for all optical ports in the opposite direction until all optical connections are made (i.e. 1st Unit's ADAT Optical IN Port 1 > 2nd Unit's ADAT Optical OUT Port 1, etc)
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Four optical cables will be required if the second unit is an Ensemble Thunderbolt or Element 88.
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Two optical cables will be required if the second unit is an Element 46 or Element 24.
*Note - When any 2 units are connected in Multi-Unit Mode the optical I/O for each unit is no longer available. You are only able to use all analog I/O for each unit when connected.
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Once both units are connected open the Apogee Control App and both should be detected in Multi-Unit mode as an A Unit and B Unit in the device sidebar with all analog channels shown.
This example shows an Ensemble Thunderbolt (Unit A) and Element 88 (Unit B)
To monitor inputs connected through any output in your monitor section you can do this using the "Mixer" assignments.
When the Main Output is set to be "Mixer 1" in this example, this will enable direct monitoring through Ensemble Thunderbolt's Main Output 1-2. 
You will then raise the faders in "Mixer 1" under each input you want to hear.
If you disconnect either unit and want to use a single unit in Control you may see previous Multi-Unit settings in Control appearing as greyed out channels.
Click the Trash Can icon in the Device Sidebar to remove these previous B unit settings. Then your Control settings will show normally for your single unit.