I would connect the kicker charger to the Perco and set it so it charges the battery that has all the auxiliary equipment such as downriggers and such,so that while it is using energy it also gets replenished. The main engine should have its own dedicated battery for starting and the main engine should charge both batteries while you are running that engine. That way you will always be able to start your main engine and your auxiliary deep cycle battery will get charged all the time you have an engine running.
As for battery chargers, a small Sears trickle charger will perform very well,give a good warranty and costs less than most "marine " brands. I have used a $27.99 Sears trickle charger (one and the same) for the past 8 years.
Happy new year and good luck next fishing season,Cornelis