Can somebody give me some information on a trolling motor/battery hook up?

i asked this question before but i didn't phrase it right...so here goes..i run a 23 hp mud buddy motor on my flat boat....there is no reverse on these motors and i'm thinking of putting on a trolling motor just for this purpose....it would only be used in tight situations, i.e. launching, marina, etc.....now, can i connect these wires directly to my battery without fear of running the battery down?? do i need to disconnect them right after i use them, or can they just stay connected....should i put alligator clamps on the connectors and only connect them when i use them, or should i just put in another battery?? i do have an extra...thanks