My charger has options to charge @ 2A, 10A, and 15A...

It also has the option of regular, deep cycle, or gel cell...

What settings should I use to charge my batteries.  Typically I charge @ 10A / Deep Cycle... should I be charging my starting battery differently than my trolling batteries?  Will it hurt my battery if I choose the wrong setting?

If your cranking battery is a dual purpose or deep cycle, use the deep cycle setting, otherwise use the normal setting.  Same with your TM batteries, if dual purpose or straight TM deep cycle use the Deep Cycle setting.  Only use the Gel setting for Gel Cell batteries.

Ideal charge rate is 10% of it's amp hour capacity so use the 10 amp setting, since most fall into the 95 to 120 Ah rating.  If in a hurry you can use the 15 amp and it's not going to hurt it.

If you have the time, you'll get a deeper longer lasting charge with the 2 amp setting. But it will take overnight and maybe then some....

http://www.ibsa.com/www/faqs/tech_talk/maintenance/charging.htm