The biggest tip is that since your body clock will be whacked by the 15 hour time change, it really doesn't make any difference when you decide to get up in the morning. We got up at 4:30 am to get ready for the 5:30am boat. You want the early boat to see the bumphead parrot fish off of the Dropoff reef. They are amazing. It is like swiming with a herd of Buffalo on the plains. They are each about 4ft long and over 100lbs and there are hundreds of them in the schools. It was truely an awesome sight. You are in the water by 7:00am and then back to Kapalai for breakfast/surface interval. Then back to Sipidan by 8:30. You do a dive and then take an hour surface interval on the island. Finally you are back to Kapali for lunch. Three dives before lunch! You can do an afternoon dive on the reef, or just rest and do a night dive by the steps. Since Kapali is literally on stilts in the water 30 miles from shore, the house reef is really very nice. I did all of the Sipidan with my 17-40 zoom and 15mm FE, and I used the 100mm macro on the house reef. The only disappointment was when we went to Mabul and I had my 17-40mm when they guide found the pygmy seahorses. I didn't even think of trying. Instead I got a photo of someone else trying to find them. 
I recommend that you hire a guide to help with finding the Manadarin fish the first time. They are relatively easy to spot if you know what to look for, but without a guide, you will have a hard time. Oh, I would also mention that you should bring a reef hook. Our first Sipidan dive on the Dropoff had a 3-4 knot current at the end of the dive when we ran into the Bumphead school. I didn't have a hook and had to hold onto a rock with one hand and the camera with the other.
You will also likely be in bed by 9:30pm in preparation for the next day. One other thing, non dive related. The food at Kapali is very good, but they don't go in for western style desserts. Several in our group were going through sugar withdrawl. If you have a sweet tooth, you might want to bring some snacks. Also remember, you are there to dive. There isn't a lot of night life.