I've got a new battery for my trolling motor. I've used it once, and the meter on the motor says that the battery is at 50%.
Is it better to run the battery all the way down before re-charging it for the first time (and every time after that)?
Never run a lead acid (or antimony)battery all the way down. Especially a regular wet cell. 50% of capacity (in amp hours)is as low as you should ever go if you want to get max life out of it. Gels and AGM's are more forgiving (but less forgiving for overcharging).
These are NOT Ni-cad's, they do not have a memory. You will wear them out quickly if you discharge them to far. If you don't have a way to measure the amphours used, the rule of thumb is 11 1/2 volts is 50%. At 10 1/2 volts these batteries are dead. (Fully charged should be about 13 1/2 volts).
Is your charger up to snuff? Is it a good 3 stage (bulk/absorbtion and float?). Needs to maintain a deep cycle properly.