Not sure what type of battery it is...how can I tell if it's a group 24?
Group 24 refers to a physical size.
I know it says cabelas 12 volt deep cycle on the from with some green looking clouds and some lightning as a graphic. I looked for it on cabelas website but did not see it. I bought it a year ago.
I am not familiar with what Cabela's sells. If it has vent caps, its lead/acid, but then there is sealed/maint free, too. If it is a gel cell, than you may want a specific charger. gels usually look like a six pack.
The first year I usded it as just a starting battery (it says: ideal for heavy duty cycling applications, and for starting too.) using it as a starting battery and not charging it a whole season will not do damage right?
No, as long as your motor was fully charging it. If it was starting only, it probably charged it. If you ran allot of loads on it and didn't run the motor much above idle, maybe not.
Also, my charger has a "charge rate" meter on it. When I plug it in and set it at 2 amps, the meter reads 2, when it's set at 6 amps, the meter reads 4. I have never charged it on the 6 amp setting.
I think you're fine at the 6 amp, and when the meter reaches two, switch. If you want to do 2 amps, that is fine as well, just takes longer. If you do have a gel cell make sure this charger is OK.
I have run the battery. Down 2-3 times to empty....how can I tell if I've done damage?
You loose some capacity
Should I just upgrade the charger with one that indicates when the battery is charged?
Having a smart charger matched to your battery is a good idea.
How long should the battery last on the fastest speed (5) pushing a 16 foot Lowe 1648MT with 3 guys, gear, and a 25 HP MOTOR? I seem to be only getting an 1/2 to 1 hour. Is this normal for the boat and weight?