Anybody ever have a problem with their unit just turning off while drifting with the motor off? I have a new battery ($300 Sears beast that people recommended) which is fully charged. It still occasionally turns off when you start the engine but most times just won't stay on continuously.
I would run some larger power wire direct to battery (dont forget the fuse). Or better yet, just down from the main breaker.
What might be happening is voltage drop across the power cable, there will be current flowing when the unit is on, if the power cable, and the place you are getting power has a little too much resistance, you will drop voltage. That could be enough when cranking to reboot the unit.
Lowrance units are particular about supply voltage. If it drops into the low 11v range you will see them shutoff like this. On your Lowrance set it to display the voltage on the display. This is the voltage the unit senses as its supply. After a full charge of your battery, turn it on and check what the display shows. Your battery should be in the 12.5 to 12.9 volt range. As you battery is used throughout the day watch the voltage display to determine where its shutting off. When you crank the motor, watch where it drop too also. It will be very instantaneous but will display briefly before shutting off.(I have witnessed this)
It is highly likely your overall system voltage is dropping temporarily during cranking or after continued use of your electronics, including potentially your trolling motor to a level that the Lowrance does not tolerate. You're only option is to get the lowrance on batteries that are not dropping to the levels that it does not like. You may find it runs fine at 11.1 and shuts off at 10.9.
Without knowing your exact setup, its hard to advise, but in the end its going to be about having a constant supply voltage to the Lowrance that it is happy with. It may mean moving other items off the batteries to other batteries to give you all day operation.