Our problem is wewer OR rotting smell is coming from side sink (kohler) in kitchen. We only use it for drip drying. However, typically dish water with food scraps pools in main larger sink. When we run the disposal to clear, we see back flow in the side sink. This we think is disposing scraps that are rotting above the trap.

Could the side sink trap seal break from a siphon of running water through main?

Pipes diameter is standard. The disposal empties into short 3 inch run, then a trap, then a 6 inch run which empties into black drain pipe. Three inches aft of main sink trap, along the horizontal run, there is a tee. The tee is rotated at a 45 degrees upward (NE), a right angle off the tee and again horizontal. The side sink makes a right angle 8 inches, then a trap, and empties into the tee horizontal.

The side sink trap is higher than the main sink trap (within an inch).

Picture attached.

Our goal is to create a space for a waste can. Use the side sink for water drip drainage, and the main sink for cleaning...

Thank you for your guidance!

What you have now is a HomeOwner's version of Two-Part-Waste installation. Simplify it. Use one P-Trap. See the photo...
Also, I am noticing 3 joints on the sink side drain that are "open" and not sealed properly. Any leaks, lately ? How is that sink side draining ?