For me and my 40 hp Mercury 2006 using deep cycle is a big no no. After my original battery for cranking went bad after 3 years I thought it would be smart and use a deep cycle. Well that smart move burned out my charging system and lost $800 dollars. If that wasn't bad enough I thought I had a bad charging system so I left the deep cycle on cranking. Guess what I had to get another charging System. After I burned out the second one. My mechanic called customer support of Mercury and he found out that never use a deep cycle for cranking with that motor model. The charging system cant tell when it is full or does not need to charge so it runs 100 % all the time and it burns out. Mechanic said he should have caught that so second charging system he only charged me parts.

Now to answer your question. My trolling motor has two deep cycle batteries. I did try to move the accessories from cranking to deep cycle but it made a wrong reading for fuel. Don't know why it does that it just does. So I put the accessories back to cranking. I have a dedicated battery for livescope and 12 inch Garmin monitor. I don't run accessories to much so it is not an issue.