Batteries died

So then it only takes 1 bad battery to kill the other.

Tyler,
As Duane mentioned, do have the batteries load tested as it's really the only test that truly tells the battery condition. Taking a static volt reading on a battery is pretty meaningless. If that 10 volt reading on your boats voltmeter was with the engine running, then there's something going on with your alternator. It should be removed and tested as well. Your auto supply can do that test too. No, using a VOM will not draw down a battery. Regarding starting and deep cycle batteries, the deep should be used to power the sound system and the starting to run the engine. How are they connected and do you have a "perco" switch connecting the two batteries?

I had a weird event happen this weekend with my 2002 super air nautique TE. We hit the water and everything seemed ok. I did notice my blower motor wasn't working properly during the launch and the start to the engine seemed a little dull. We wake boarded for 3 sets then took a break for about 45 minutes. We listened to music while floating. As we started the 4th set, the perfect pass would not dial in properly. The audio also started to not play correctly and a lot of static occurred especially with the sub. I checked the battery gauge and it showed just above 10 Volts. We stopped and anchored down and jumped in another boat. We came back an hour later and the boat barely started. As I pulled away I gave it throttle and I could only go about 5-10 mph before the motor would muffle out and feel like it was going to stall. I finally got to the dock and shut down the engine. I tried to switch the batteries around and at this point to see if one was dead. I tried to start the boat with the batteries swapped and it wouldn't turn over. We put the boat on the trailer without getting the motor started and it was a disappointing ride home.

I'm not mechanically sound with my boat yet as I've only had it for less than a year and I am newbie when it comes to working on boats/diagnosing.

Any ideas what this would be? Alternator?
The batteries are 1 and 2 years old. I had them inside all winter and charged them occasionally. This was my third time out this year. I had no issues last year ( only ran it for about 30 hrs). I didn't have issues until this weekend. I charged my batteries today with a mini charger only having 1.5 amps. Right now one battery is at 12.38 and the other is at 12.08. While checking the 12.08 within 2-4 minutes it was down to 12.00. Not sure if using a meter draws any power if it did you'd think it wouldn't draw battery down that quick.