Check out how this rig looks from the top down here.

The first thing to do is tie a leader with a live bait hook at the end.  Usually a size 4 hook is good, tied with a palomar or clinch knot (snells aren't good for live bait rigs). Even better, and my personal preference, is a hook secured with a perfection loop, which allows the bait to move more freely. The hook line should be a minimum of 12 inches long--20 inches would be overdoing it. On the main line, insert the bead, bobber, and egg sinker and tie a safety swivel snap at the end. Attach the hook leader.

Before you put on bait, you'll need to adjust your rigging to the depth. At Berkeley Pier, the average depth is 8 feet plus whatever tide is on it. You will be guessing/estimating the point at which your hook will be about 6-12 inches OFF the bottom. This is important because halibut are ambush fish and strike from below. If your bait is dragging on bottom it will seriously lose effectiveness. You'll just have to work on trial and error until you feel comfortable with the setting. Once you're pretty sure, set a bobber stop above the bead.

Now put on your bait. If it's a live shiner perch, hooking through the nostrils is a good way to attach it. Some people like to hook it through the skin right next to the dorsal fin because halibut bite from the tail first. But bait seems not to last as long this way; also there's a chance it will slip or tear off. (A remedy for this is to use a cut square of rubberband and place it under the barb once you've hooked the bait.) Live anchovies are used the same way. However, frozen anchovies can be effective and are easier to attach because you're not worried about injuring them. Thread your hook line (a piece of coat hanger with the top notched will work better than any threader purchased in a shop) so that the hook will be next to the tail. You can use elastic string to keep the bait on more tightly.

When you cast, don't try to get your rigging out too far. About 10-15 feet out from the pilings is sufficient. Halibut will hit anywhere along the pier, but the best places seem to be near the bathrooms and the cleaning tables because the gray water runoff attracts bait fish and their predators. But change locations if you're not getting anything after an hour. Finally, it's always a good idea to see what other anglers are doing. When the halibut season is in full swing (somewhere between late March and July when they come into the bay to spawn), there will be as many as thirty "regulars" lined up. They are irritable, rough-hewn fellows, but they will yield crucial information if you ask. This rigging is only one of many possibilities. Experiment and observe and you should do well. 

**Keep in mind that lighter and smaller is preferable to heavier and bigger.  The sinker and bobber illustrated are on the very highest end of the scale.  If you are confident and can use half an ounce on a small float, so much the better.** 

UPDATE 5/2015: Here are some photographs that illustrate the slip bobber as I use it on a light setup.  Hope they help.   

  Berkeley Pier 2008 (all pictured fish caught by yours truly; released 3x as many that year)