The limitations of your interface are going to be a constant problem when your dealing with signals from multiple sources simultaneously. You have a couple of options though. Either replace the interface with one that has more ins and outs, or add a small analog mixer in front of your interface. I ran a small 4 channel mixer for a while, then later went to a 24 channel mixer and ran this way for a long time. This setup is fine for personal use where you really only need to record only a single track at a time from different sources. A single MIDI in-out is another limitation, but can often also be gotten around. Again if you have more than one MIDI instrument you’ll only be able to record one at a time, but playback should not be such a problem provided your instruments have Thru outs. The audio from each instrument goes to a separate channel on the mixer and is heard through the monitors (which would be connected to the Mixer outs) oblivious to what signal if any is going to a track in cubase over your interface. If this concept appeals to you we can discuss it in more detail if necessary.
For now lets look at your problem afresh.
Forget External Instrument and everything else suggested previously.
What you need is 2 MIDI connections between the Juno and the interface (crossed in to out, and out to in as usual). This will facilitate midi data to be recorded to a midi track in cubase, and similarly allow these same signals to be transmitted back to the Juno. Once the midi is recorded. you no longer require the midi cable between the juno out and the interface in!
With MIDI Thru Active in Cubase Prefs, and Local turned off on the Juno; with headphones or monitor speakers connected directly to the Juno, you should be able to hear it playing. If you want to record the audio from it then you need to connect the audio out of the Juno to the Interface In and record the signal on an audio track. (Once the audio is recorded, the midi track can be deactivated!)
If you have your monitors connected to the Interface outputs then to hear the Juno you will need to activate the monitor button on the Juno audio track (once recorded this button should then be deactivated).
If you were to use a mixer in the above case, the Junos audio would be connected to a given input(s) on the mixer, and these routed to the monitors. Pressing a record button on the mixer, or routing to a sub channel or send (this depends on the mixer) would route the signal to the audio interface for recording. The interfaces output is also sent to the mixer via a dedicated mix or listen input or standard inputs and thus to the monitors.
I hope the above makes things clearer, and not cause more confusion.
