On page 2 of my album you can see some pics of a yamaha 15 h.p. four stroke mounted to starboard, on a mini jacker, next to a yamaha 80 main which is the physical size of the 100 h.p. Just detuned to 80 h.p. The kicker clears both the main engine and the Bennett 120 sport tabs. The tiller will barely hit the splash well wall to starboard and the main to port in a full locked turn if I don't lift it up. The kicker will turn the boat tighter than the main.
I prefer running the kicker out back in the fresh air. Not interested in the connector bar to the main. I always run with the main engine raised and as mentioned makes a great back rest. Even therapeutic when that big engine cover is warm and you cover it with a wet towel. I often sit on a boat cushion on the lazarette and steer with my left foot. When the throttle tension is set you can even control the throttle and steer with one foot. (safety lanyard around ankle) You have good visibility looking thru the cabin windows this way. I can even see the sonar at the helm thru the aft cabin window.
If both batteries are to starboard as mine are it will list slightly but it is no big deal. The boat can be leveled by moving a cooler, spare anchor or other gear. At faster speeds the trim tabs handle it. This arrangment works good especially if your swim step is already to port. I would recommend moving the batteries to port and keep the kicker to starboard if faced with the decision. But like I said I haven't felt the need to move the batteries. My bait well is used for dry storage, extra ropes and such. So, if I did move batteries up pops another problem.