Jeff and Diane- I assume you're mounting the engine on the transom, along side the new Yamaha 90, and not on a separate bracket (motor mount) further off to the side directly behind one of the lazarettes.
If you're going to mount it on the transom, along side the new motor and therefore steer and operate the throttle with the tiller handle, your only option is to mount the kicker to the left side of the main (starboard side of the boat) because the tiller handle is on the right side of the kicker. There's simply no room to swivel the tiller handle if you mount it to the other side. Mounting it on the right (port side of the boat) would require the separate motor mount and a cross-linking steering arm/link to the main motor.
The trick is to mount the motor far enough away from the main to allow it not to inhibit the turning/steering of the main, while still allowing the kicker enough room to swivel and steer and not bang into the side of the transom well. Too close to the main and you lose some of the steering/maneuverability of the main, too close to the other wall and the kicker loses some of its maneuverability. The exact way this works out depends on the physical dimensions of each particular combination of motors.
To accomplish the above, or find the sweet spot, mount the kicker somewhat losely on the transom, and move it back and forth, right to left experimentally until the main can swivel fully and you have preserved the maximum amount of kicker "swivelability" at the same time. Be sure you save room enough so that you can tilt up and lock the kicker out of the way when going fast with the main motor to avoid dragging the lower unit of the kicker. Often a compromise is necessary. For example, on my Johnson 15 and and EvinruEvinrudet up, the kicker maneuverability is about 75% of the normal maximum to allow the main to fully rotate, so you might not get a perfect 100% + 100% combination. Maintaining main motor maneuverability takes priority.
If this arrangement is unduly restrictive on the kicker's steering, you may want to consider a auxiliary motor mount for the kicker in the future. Then you would have your choice of which side on which to mount it.
If you have a rubber mounting pad to place over the transom to protect it from the kicker's mounting bracket and clamps, this would help insure you don't mar the finish on the motor well.
Make sure you have room to attach the gas hose to the kicker once it's mounted plus any other required connections (electrical, if required).
If you like the placement of the motor and the arrangement, you may want to consider for the future a steering link that will connect the two motors, either at the front or the rear, to allow you to steer with the helm's steering wheel as opposed to the handle on the kicker. You'll still have to operate the throttle and shift mechanism from the motor, of course, unless you opt to install remote controls for these.
Sometimes the final placement of the kicker is affected by a number of factors such as the desire to place it on the opposite side of the boat from a single person/operator to balance the weight distribution of the boat better, or to avoid interference of some other accessory, such as a swim step, but you can deal with much of this later. For now, get it mounted where it can serve you as a back up motor and a trolling motor and take your time to make a final decision carefully.
Hope this includes everything and helps! Joe
:wink 
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