Hooking up the battery charger terminals in any order is fine as long as they are tight. If you have a straight 24 volt system (jumpered at the trolling motor receptacle) make sure you disconnect yor trolling motor plug otherwise it is (possible) that strange return path in the charger could be created.
Best thing I can recommend is to get a volt meter and check the terminal voltage of your batteries before and during charging. Thats how I discovered my charger went belly up. A very cheap but functional digital volt meter can be bought at Harbor Frieght Tools (its made in china :-( , but some folks dont/can't fork out 50+ bucks for a better one). As Matt said, most electronic battery chargers will not turn on if the battery is too low, has a bad cell or shorted cell, or has reversed connections.