So does my 97, I have had at least 30 boats in my lifetime and I always run on Both. This time I followed the directions but port motor shows about 2 volts difference when I run the switch on 1.

Heading out today and will try both. Non EFI motors

Port on 1, Starboard on 1, most Cigs parallel on start. Ports 1 is Starboards 2. Starboards 1 is Ports 2. So if you put Port on 1 and Starboard on 2 you only use one battery. This is in the owners manual.