Nothing wrong with shooting up. I think it works. perhaps turn the strobes off next time. if the subject isn't very close, you don't get the benefit of the light but all the downside of lighting up particulate inbetween.
I would try it in B&W. Very hard to edit otherwise given the amount of backscatter.
nice hammerhead encounters. Very nice images overall. what are you using for wide angle?
Very odd behaviour for the lens. are you saying you can't do back button auto focus? I don't have the 50mm nor the nex 6 so if this is redundant to you, i apologize.
for macro, I typically have my nex 7 set to manual focus and the AEL/AF/MF button set to af/ml control under the custom keys settings. So => Menu/Setup/Custom Key Settings. I notice the NEX 6 only has an AEF button where I have a toggle. That said, I would have thought it would be customizable. I would think the trick would be to move af to a back button process and take the lens and shutter out of it.
Hopefully this helps and its not something so obvious that you've already tried
I've been a few times and really like Birds Underwater and they have come highly recommended by others here too.
Birds is great as they go out earlier than a lot of other tours, so you get one on one time with Manatees.. Definitely bring strobes & fins. Strobes bc when you first get in, its dark.
Water is a constant 72 degrees f due to the springs. Air temp can be in the low 30s-60s. widely variable. keep in mind you are not swiming much, mainly just floating, so you will feel the cold esp when you come up. I'm a native floridian so 5mm-7mm would be my choice. Some of the guides go in Dry suit, but that is overkill.
There are loads of hotels around. Do a google search but all the holiday inns, quality inns, etc are covered there.
As said previously, the manatees will seek interaction if you mind your own business. they they like puppies. relax and they will come to you.
One other thing. its illegal to submerge while swimming with the manatees. so practice "shooting from the hip" if you want upward facing shots.