Hey mate,
My .02c comment would be that your Ctek charger @ 15 amps would struggle to charge a 24v system.
They are a good charger but charging 24v will require a charger with a higher amperage output.
You could isolate the batteries by disconnecting them and charge them separately, but this would obviously take twice as long as using a charger designed for 24v.
If I may ask, what is your reason for upgrading to a 24v minn kota?
I run a 12V minn kota with a deep cycle gel battery and have never had any issues with a flat battery or lack of power. I usually only recharge after 3 or 4 trips.
Recently I took the boat out after a 9 month lay off and still had 3/4 charge in the battery with no issues on the water
Interested in your response.
Cheers
Choicebro