You'll rely on autofocus to focus the lens. Your housing needs to accommodate a zoom ring for a zoom lens. For a prime (macro) lens, you can get focus rings instead.
How you shoot depends a lot on whether you are using strobes or not. If I'm shooting with strobes, I'm pretty much always in manual mode, playing with aperture for depth of field and strobe power for exposure. I've gotten used to manual strobe exposure too, after years of TTL. Not that hard, but be prepared in any case to do a lot of post-processing, so shoot in RAW.
When I shoot ambient, typically with a wide zoom, I'm sometimes in aperture mode, but often I'm in manual mode just like with macro with one exception - I turn on auto-ISO. Which is the same thing as playing with strobe power in a way.
The reason why I shoot manual is that I really want to set certain minimums and control them. I don't want shutter speed below 1/160th typically, in order to reduce blurred fish. Over 1/200th I get banding in the strobes, and that also means less ambient exposure. 1/160th is where I end up in compromising between strobe, ambient and ISO. Aperture I almost always use for depth of field in macro and corner control in wide. I never have enough depth of field in macro, and even at F5.6 I pretty much have huge depth of field at 16mm. But getting those corners sharp.... (I'm shooting a D850 with Nikon 16-35vr behind a huge 230mm dome port. I had to always crop edges until I added a Sea & Sea Internal Correction lens/filter. Now I can shoot at F5.6).
And I want to control my ISO very, very much, especially with macro. I want my ISO set to 64 if I have enough light. I use the extreme dynamic range to give me options in post-processing. Those options disappear rapidly as the ISO rises.
So there you have it - fix shutter speed, fix ISO (except ambient if you have to), fix aperture to the scene, and ... you're shooting in manual. Except maybe TTL flash.