I have a Dual Pro 2 bank onboard charger, and after putting my batteries back in my boat toady, i noticed something odd.  First off, when I plug in the charger, the exterior indicator lights dont light up.  Also, when I went to trim the motor down, the lights lit up.  I put the positive and negative wires on the two trolling motor batteries and nothing else is on them.  What am I doing wrong?

That doesn't sound right at all if they are only hooked to the trolling batteries unless you have a common ground between them some how. Might want to go to there site and see what they say. Good luck

Did you say that you have nothing but the charger leads on the trolling motor batteries and the charger lights do not come on - but when you trim the motor up the charger lights come on?  That's bizarre since there should be no connection between them... (unless you are running a switchable 24/36 system that uses the cranking battery as the 3rd - but I doubt that is the case)

I suggest you double check you connections..

If you haven't done so already, when all is wired properly, it's a good idea to place a piece of tape by each battery terminal (1,2,3,4,5,6...) and mark the corresponding connections with the appropriate number.  This helps reduce the chance of mistakes when hooking it all back up. 

ok....thisis too funny.  I double checked my connectons again today and I cant figure it out.  Then I honked the horn, and the battery indicator lights came on!  I guess I'll be contacting the company for assistance.

Is it possible that mice nested in the boat while it was laid up for the winter?

Nasty little critters love to gnaw on things.  Wiring can be like candy to them.

Double check all the grounds.  Faulty grounds can cause all manner of funky things to happen when it comes to electrical stuff.