I don't have your D50 setup, but I do have a YS-90DX that I use in manual and TTL with certain cameras. Some suggestions:
1. Use a fiber optic cable. Nice and simple, with limitations of manual only.
On the YS-90DX set SLAVE to enable the optical sensor, and use one of the two strobe manual settings: PRE setting if your D50 is in P, A, or S modes (probably does not work with the D50), otherwise the ON setting if the Camera is in M mode (recommended). I'd start with a very low strobe power setting, the lowest -7 perhaps. The proper power setting depends on your camera aperture, distance to the subject, visibility and general lighting at your depth. It's very much a trial and error process. The YS-90 is overpowered for macro, so you really have to reduce output. Try it on land with a macro subject, then expect you might have to increase power a little in the water due to visibility conditions.
2. Use optical TTL, with Heinrichs Weikamp Digital Adapter - more versatile
Heinrichs Weikamp Digital Adapter
The DA is just a slave sensor you affix in front of your camera flash (use black Velcro with holes). It gives you a Nikonos connector to connect to any Nikonos compatible strobe -- you need a wire cable and suitable strobe. It will work in manual mode only with just about any strobe with a Nikonos connector, which is about 80% of the strobes ever built. However, for TTL flash you need a strobe that works TTL with your camera. It so happens the YS-90DX does not work TTL with the D50, unless you have the MikeDive mod (below). On the Heinrichs Weikamp site is a lookup table of the strobes that have been measured to work TTL with your camera and most others too. As far as I know, this is the only site on the web where such a compendium of Camera strobe requirements and strobe capabilities is published -- a tremendous asset to us all.
HW
MikeDive Mod to certain YS strobes
The YS-90DX strobe timing is not compatible with the TTL flash timing of your Nikon D50, unless you have MikeDive modify the YS-90DX. Here's the problem. As sold, the YS-90DX has a minimum time between flashes of 30,000 Microseconds, but the Nikon D50 and many other Nikons emit 2 preflashes that are closer together, 8,000 Microseconds. MikeDive in Germany can modify the YS-90DX to for a shorter recovery time of about 2,000 Microseconds, which is as fast as anything on the market.
http://translate.google.com/translate?hl=en&sl=de&tl=en&u=http://www.mike-dive.de/
3. Add a Heinrichs Weikamp TTL converter to your Fantasea housing.
This gadget translates Nikon iTTL strobe signals to Nikonos UW strobe signals. It requires a new hole in your housing and provides a Nikonos bulkhead connector for most strobes. You buy his OEM Nikon TTL Converter and a Nikonos bulkhead connector, and drill an appropriate hole in your housing for the pass through.
http://www.heinrichsweikamp.net/#/en/oem_solutions/
MikeDive does custom work and he sells the Heinrichs Weikamp line too, so I expect he could handle everything. MikeDive is a true craftsman, and the end result is professional. In the end you would have a very excellent housing, and a strobe that could work with just about any camera in the future.
Introduction to Underwater Photography with DSLRs
MikeDive has a rather nice introduction to Underwater Photography with DSLRs, highly recommended while you are visiting his site.
http://translate.google.com/translate?hl=en&sl=de&tl=en&u=http://www.mike-dive.de/
