The YS90 + YS120 are used on my film setup (Nikon F80s on NX-80 housing)
do you use them to shoot manual or ttl?
I use 2 YS-110s on my digital setup (Nikon D300 on MDX-D300 housing), they are used manual all the time (no TTL converter).
On the film setup I used TTL on macro setups.
what do you set on the camera and the strobes when you shooting on either setting?
Nowadays I dive mostly digital (film housing bulkhead needs to be fixed).
I don't memorize my settings.
When I buy the camera I run the Menus several times creating menu banks for Topside and Underwater (Macro & Wide).
I dive in mode M 90% of the time. In Macro I start out on 1/250 and f/16 and work the flash power on the first minutes of the dive, but from them on several things can (and do!) change: Flash Power, Aperture, even the AF Mode Switch. I do play a lot with the AF Sensor Selector (thumb-pad) as most of my shots are in single AF Area.
do you just set your shutter to 60 only or what else do you set that to?
Normally I start at the Flash Sync Speed, but from them on I might slow it down to get some ambient light, or might even shoot in A mode to get a panning effect on running fishes. But it has almost nothing to do with hand-held speeds, as most of the macro shots will be "frozen" by the flash at more than 1/1000s