I have a 2020 Feedom 307 which i purchased earlier this year. It is the same hull as the Canyon, is equipped with the bow thruster and has 4 batteries. The first month I had the boat I did not have a power cord for it. And had no issues with the power sterring or the bow thruster, they worked every time i fired up the engines. I did finally buy a new 30amp power cord, mainly to make sure the batterries would not get run down if the bilge pumps kicked in for too long.
Your issue sounds like you have some kind of unexpected draw on your batteries. Do you use the battery selector to turn off the batteries when the boat is moored? I've learned that is the best way to keep the batteries healthy.
i also have no idea why you need to keep the batteries on just for the bow thruster. I respect Seasicks comment "The bow thruster is probably powered by a battery or batteries that are not charged by the outboards." However, I can't imagine GW would wire the batteries in this manner, as it would seem to be sure to fail for many GW owners. You may want to check with GW or get hold of a wiring diagram for your boat.