Here is the formula that I use:
1) Set aperture you want for DOF and sharpness For macro F11-F16 for WA start at F8 then back down if necessary.
2) Set shutter speed for bacground lighting, I Meter off the blue water then go down a stop for a deeper blue (personal prefereance). If this is less than 1/100 s then back off on aperture.
3) Adjust strobe power for subject exposure. I Don't have to do much here since I'm using TTL but sometimes I tweak flash exposure compensation.
Sometimes on white sand the above preferences need to be adjusted if the values fall outside the range that TTL can compensate for. Then you have to adjust either aperture or shutter speed. If your depth changes you may need to re-evaluate shutter speed.
I always shoot at base ISO for low noise. In my case ISO 200.