A deep cycle generally isn't necessary, but can be better for long periods of discharge - sitting at anchor with the stereo or lights on for hours at a time, etc. Many (most?) of the FW bow riders are delivered with a pair of "dual purpose" batteries which are a compromise between starting and deep cycle (and in my experience, a great choice). The original dealer who sold your boat may have had a different opinion about what was best, or the original owner may have requested the different batteries. I assume, being an '07, they are still original - and if so it's time to replace them.

The alternator will charge both if you have the switch set to Both. Different people have different opinions about how to maintain a dual battery setup. The method I choose (with a pair of dual purpose Interstates) is to run on 1 for half the day, then switch to 2. I never run on Both and wouldn't, unless both are run down to the point that neither will start the battery by itself. I like knowing which battery is "1" and which is "2," so I've added labels to the switch to identify which is which.

The only hard & fast rule is, NEVER move the switch to or through the Off position while the engine is running. Alternator damage will result.