Is there any way around this perhaps?
I'm using a 8" dome and a 15mm fisheye. Underneath the water everything looked like it was in focus with only aperture f4.5 in this picture.
Perhaps where you focus can have an inpact. Prefocus on a point a third into the picture?
Manual Focus, only way.
If you Auto Focus your Focus Point will pick up what ever it's locked onto, underwater area/above water area, you have to Manual Focus for the best compromise between the Underwater section & Above water section.
Another trick is to wipe your Dome (The Housing Dome, not your other dome), with "Rain X Glass", helps make the water droplets not stick to the Dome and becoming a problem with blurry spots in the Image.
Over/Under shots done well are a bit of a suck & sea, lots of practise, but always with Manual Focus, f/16.
I use a Seacam Housing with a 5DMKIII + 8-15f/4 or 24f/1.4, 8-15 @ 15 & f/16, the 24 @ f/16.
Have a look at some of "Lemmyshowyou"s Images on the 1Dx site, maybe PM him and I'm sure he will gladly give you some more advise.