Hey, Gotcha. Let me try to help.
DS-50: Nifty little strobe. It's switch has three positions: Off, Manual, and TTL. The "Manual" position is for use with hardwired systems only. You would never use that with your camera. With your camera, you have two options to establish communication between your camera and the strobe, and with either one, you will switch the strobe to TTL. Ikelite sells two separate controllers for the DS-50 and DS-125. You can use either one with your set-up. The TTL controller mimics what your camera's internal built-in flash does. It pre-flashes and then starts and stops in sync with the camera's little flash, which theoretically is gauging how much light it needs to expose the picture properly. The manual controller makes the DS-50 work very similar to the Sea & Sea YS-90DX, in that, it ignores the pre-flash and fires on the exposure flash. The amount of light delivered is determined manually by the photographer and controlled with a 12 position switch. Even though it is called the manual controller, when you have it connected to a DS-50, you will switch the DS-50 to TTL (I know, that is really confusing).
YS-90DX: Pretty much like the DS-50 with manual controller, except the manual controller is built into the strobe. It ignores the pre-flash and fires the strobe in sync with the camera strobe, but you have to tell it how much light to deliver.
You can read more about the YS-90DX at: http://www.digitaldiver.net/photoinstindex.html Hit the link for "Choosing and Using Underwater Strobes". Unfortunately, I wrote this before the manual controller was out, so it is not discussed. I am planning on updating it, but will probably wait until the combo controller is out.