Needed information:
Computer type and operating system
Yamaha USB-MIDI Driver version
Cubase version
MIDI Port Setup
Remote Port Setup

We know you say you have them setup correctly, but you don’t tell us how they are set. That information is helpful, just on the strange outside possibility you don’t have them set correctly.

My usual setup - Start the Stand Alone editor and bring online. Open Cubase and use the S90XS as my MIDI input source for various VST's including the S90XS itself.

This statement is a bit troubling... you can either run the the “Yamaha S90XS/S70XS Editor Standalone/VST” as a Stand-alone or you can run it as a VST... but not both simultaneously. Please run it as a VST. Do not launch it Standalone. Launch it only inside Cubase. DEVICES > VST INSTRUMENT > Rack Instrument > External > S90XS/S70XS VST
It will ask you if you want to create a MIDI Track for this VST. It will be assigned MIDI Out = “S90XS/S70XS VST-MIDI In”. All subsequent MIDI TRACKs should also be assigned to that as their MIDI Out.

The “Remote Editor” is a separate application... it is unclear if this is what you mean. The Remote Editor allows you to setup and control various VST plugin synths using templates you can recall and modify. (This is a separate Editor and always runs separately).
The other Editor is like an S90 XS editor/librarian for Voices and the current Multi... and runs as a VST INSTRUMENT.

Running it as a VST means it can be configured to automatically save and restore your instruments settings when save and restore the Cubase Project (.CPR).

No mention is made of the [DAW REMOTE] button or the selection of Cubase as your Remote DAW. (Both of which must happen).
I know that this may all be clear to you but we have to check all the boxes before we can conclude it’s not working due to anything other than a setup error.

Let us know.

Thank you Bad Mister

Needed information:
Computer type and operating system : iMac 3.2 GHz Late 2012 , Mac OS Siera Version 10.12.6
Yamaha USB-MIDI Driver version : V1.3.2
Cubase version : Cubase 8 PRO V 8.0.40
MIDI Port Setup : In - YAMAHA S90 XS Port 1, Port 2, Port 3, Port 4, Port 5 (All active)
Out - YAMAHA S90XS Port 1, Port 2 , Port 3 (Inactive) , Port 4 (Inactive) , Port 5 (Inactive)
Remote Port Setup : YAMAHA S90 XS : Midi Input : YAMAHA S90 XS Port 2 , Midi Output : YAMAHA S90 XS Port 2
Track Quick Controls : Midi Input : YAMAHA S90 XS Port 2 , Midi Output : YAMAHA S90 XS Port 2
VST Quick Controls : Midi Input : YAMAHA S90 XS Port 2 , Midi Output : YAMAHA S90 XS Port 2

I Followed the MIDI USB Quick Setup guide to install , but what confuses me is when I select Devices - VST Instruments - Add Rack Instruments , I have 2 options to choose from : Option 1 : External - YAMAHA S90XS VST
or Option 2 : External Plug-Ins : YAMAHA S90XS (No VST behind the name)

I think I have been doing it wrong because that is how I learned to connect when Cubase 8 was released ( the first version ) and I have been doing it that way all along. I had to save my settings in the S90 XS Editor stand alone for each project because those instruments settings were not saved by Cubase.

I am not a very tech savvy guy, sorry, so this is all a bit confusing to me, give me PlugnPlay and I'm happy. And if I find a way that works for me I stick with it because I struggle for so many hours to try and figure out what settings to do when a new version of something come out.

I only saw a few minutes ago there is a new article on your S90 page about the S90 Editor VST. I will follow that.

Then back to my actual problem , how can I connect the sliders, ModWheel , knobs on the S90 to control automation lanes in Cubase? I have seen so many Youtube videos where the users demonstrate setting it up, clicking on a quick control lane of a Instrument track , click the learn button, then he slides a slider on his hardware and it works. But when I try that , just no reaction. So for example, I have recorded violins from EWQL Symphony Orchestra and now I want to record the Modulation or the CC11 Expression and I want to use the S90 Modwheel to input that, how can I do that?

I have never used DAW REMOTE button , (just for information) because sometimes I use EWQL Symphony Orchestra together with the piano from the S90 and I don't think I can exit the 'online' state of the S90 editor because then the piano won't play anymore in the mix.

I will really appreciate your help.

I Followed the MIDI USB Quick Setup guide to install , but what confuses me is when I select Devices - VST Instruments - Add Rack Instruments , I have 2 options to choose from : Option 1 : External - YAMAHA S90XS VST
or Option 2 : External Plug-Ins : YAMAHA S90XS (No VST behind the name)

The one labeled VST refers to the Yamaha S90 XS/S70 XS Editor VST... The other refers to the XML VOICE LIST installed into Cubase. Clearly, you want the Editor VST. It is better than the Voice List because the Editor automatically updates to include your User Bank sounds as well as the Presets.

MIDI Port Setup : In - YAMAHA S90 XS Port 1, Port 2, Port 3, Port 4, Port 5 (All active)

Yes, but in the column marked “In ‘All MIDI Inputs’” you should only mark Port 1 for the S90 XS itself, and Port 3 if you have an external MIDI device connected to the 5-pin MIDI jacks of the S90 XS. Port 2, 4 and 5 should not be marked as MIDI inputs on this screen.

[DAW REMOTE] should be used when you want to use the S90 XS as a remote control surface for your DAW. If the button is not activated, you can’t expect to use the S90 XS as your remote controller. Please see the DATA LIST Booklet (page 96) for Remote Control Functions already assigned.