Re: Proper method to charge marine battery
I am an electronics eng and I can tell you that a regulated charger, or 'smart charger' will
not hurt the system if you leave the battery leads connected....
I do it all the time with my car. I work away, sometimes for up to 3 months. If I leave the car the battery is as flat as the proverbial when I get home. I checked the system and with nothing on and all the doors closed it still sucks 170mA.

I have a very dumb, unregulated trickle charger, and a mains time clock. I plug the charger into the timer, which is set to run for 1.5 hours every 12. I put the charger on the intake manifold, connect the leads to the primary battery, close the hood and walk away. When I get home, I pull the charger off and drive the car around until I'm ready to go away again....
Sometimes I forget to turn off the isolator in the boat and one of the batteries drops a bit (not when I'm away. I double triple check everything before I go) so I just throw the trickler on for a couple of days.
I have never disconnected leads, never will and don't see a need for it....
As for leaving a charger connected when you start the engine... done that too... no problems. Waterinthefuel, I suspect you had something else amiss at the time. If the voltage from the charger was higher than the engine output, then the diodes would be reverse biased and would not conduct. If the output voltage of the engine was higher, then the charger
may have sucked the extra electrons (just like a flat battery does

), but the output current of the engine charging coils is way lower than the rectifier rating (typically the rectifier is rated at 25 amps and the output of the engine alternator is about 9 amps).
Chris.........
If anyone disagrees with what I have said, please explain the difference between having a 14.2 volt charger (voltage source) on the battery leads and having a 13.2 volt battery (also a voltage source) on those same battery leads!
The reason the service manuals tell you to disconnect one or both leads is CYA (not yours, theirs), nothing more....