I'm assuming you're not using a strobe? In that case, I basically just leave the camera with the functions menu up - I think it's the second button down from the top? And the arrow keys move it to white balance, and a flyout menu comes up to the right. The farthest setting to the right is "custom". (You can just press the left arrrow once and that takes you over to the right). Point the camera at a white object - most people use a dive slate - (I wear a white rubber dishwashing glove once I got tired of the white card flapping around), and hit "select" (I think that's it - the button right below the arrow buttons.) As long as most of the frame is filled with white, it's fine - doesn't need to be focused or anything. Just pay attention to the angle you hole the white card at - you want a similar angle as your subject.
You should re-balance as often as possible - while shooting video, I rebalance before every shot if there's time, since the direction you're facing will change the light, as will the depth, amount of overhead stuff (i.e., kelp), etc.
You can also use a red filter, but I couldn't ever find one for the S1 housing. Plus, it just applies a single strength of correction, no matter what depth you're at. Custom white balance does the same thing, but it adjusts for your exact conditions.
On that camera, I never did get it to take really good still photos since the shutter delay is sooooo long, but others on this forum have had better success. I believe I got the best results in P mode at ISO 400, but at 400 there is a TON of noise in the shots. Maybe you can get away with less ISO if you have more light.
Your camera takes really primo video though - get a 1g card and set it on the best video resolution (640x480, 30fps) and you'll get really decent video and it is waaaaaaaayyyyyy easier than still photos.
Good luck! It's a good little camera.
Taxgeek