Step 1: create an External Instrument Channel Strip in MS. Choose the correct MIDI port and channel.
With this selected and setup for MIDI input in MS you should hear the Yamaha if you plug some headphones into it.
Step 2: get the audio back from the Yamaha into MS.
Connect some audio cables from the Yam outputs to the inputs on your audio interface. Select these inputs in the External Instrument channel strip you created in step 1.
You should be good to go.
Sorry if I'm misunderstanding what you've written, but I'm really looking for how to make program changes on the *Yamaha* through the patch list in MS. Your solution sounds like how to get the Yamaha sounds back into MS.
I think the above image capture shows that you *can* change it, but my connections between the Yamaha, or settings on the Yamaha are not correct - it's not making the program change on the Yamaha.
Yes, my instructions werre for the "basic" connect up and bring the audio back into MS (your picture is not showing up here?). I misunderstood where the issue was:
Assuming that you have the basics working, you cannot get the Yam to change internal patches from MS?
This should be straightforward (forgive me if I am being too basic):
In MS, select the External Instrument channel strip and select the MIDI Output Tab in the Channel Strip Inspector. Check the 'Send Program Change' box and dial up a PC number. MS should output the PC messages as you dial them up, and the Yam should respond (for now only within a single bank of sounds). If it does not, there must be something wrong at the Yam end (is it correctly set to receive PC messages on the correct channel?)
Next would be to try using Bank Select MSB/LSB messages to change banks within the Yam. This should work OK provided that the Yam is set up correctly.
Assuming this works, all you have to do is create Patches in MS that send the required PC/Bank messages.
Alternatively, on can setup a Screen Control to transmit PC messages.
Whilst I do not have an S90 here, I have plenty of other synths, and the MS PC changing works correctly with them.