Well, Juno 106 is a good choice if you need midi and a vintage synth. Its midi implementation is quite good.
Dont worry its very easy to set it up.
Lets first start with the midi. Yes, you will need a midi interface. You will connect the midi out of your interface to midi in of Juno, and midi out of juno to midi in on your midi interface. Then you will choose the matching port and channel of midi on your cubase to send and receive the midi. For example If you have connected juno to midi port 1, you will choose midi in and out 1 in cubase(If both midi in and out are on port 1 I generally choose matching ports so I dont confuse myself)
Every midi port has 16 channels under it by the way, but by default your equipment is set on channel one. So you can choose port one, channel one. This is so that you can connect up to 16 equipments with one midi port through daisy chaining your midi devices and choosing different channels for each equipment.
Then you will connect your juno 106 sd audio outs to your ensembles 1/4 in s. This way you can use juno to record midi data and audio data. You can also send midi to juno and record audio data. Whichever you prefer.