So my onboard charger says "no need to unhook any thing while charging" and my trolling motor manual says "unhook while charging"

So what do I do ?

Leaving the TM plugged in wont hurt a thing.

If it's a cable steer you can leave it plugged in. If it's electric steer, disconnect it. BTW, I would go with what the motor manufacturer said anyway to avoid any type of warranty issues. Better safe than sorry. 

The main thing to consider is that the charger does not want to see anything being drained out of the batteries while charging. If it is putting a trickle charge on the battery, anything draining the battery while it is trying to charge negates the charge.

 

You can leave everything hooked up as long as everything is turned off so there is nothing draining the battery while charging. A lot of people use a battery switch for this reason.

 

Something to consider... some chargers deliver an automatically variable amount of charge to the batteries. If the battery is really low the charger might deliver more current say around 10 to 15 amps, and as the battery is charging up the charger could reduce the amount of current flowing into the batteries to a trickle charge of less than 1 amp. If something else were on draining the batteries while charging it could fool some chargers into staying in the higher current delivery mode which is not good for batteries and can cook them if left too long like that.

 

When I charge my batteries I manually set the charger to its minimum level of charge so I never run the risk of the charger automatically going into its 12 amp fast charge mode because I do not want to "cook" the batteries- ever- even if I run them down low which thankfully I haven't yet.

Unplug. When I was test driving the ranger, the brand new trolling motor wouldn't work. Turns out the guy charged it with it plugged in. Destroyed the circuits in the motor. Good thing he paid to have it fixed. Unplug just to be safe.