One thing you'll want to do if at all possible is to be in Phnom Penh for the first day or two of festivities including the fantastic boat races on the Tonle Sap. They last all three days but one or two is enough.
Then head up to Angkor Wat for the Buddhist ceremonies on the last day of the Festival (actually this is a separate celebration having to do with the beginning of the fishing season). They're held at the entrance to the main Angor Wat temple at night and are absolutely otherworldly (torches, candles, flowers, and hundreds of Buddhist monks). Since the festival is on a lunar calendar, you should have a semi-full moon, which allows you to walk around within the Angkor complex itself after the ceremony, in the dead of night (10PM or so). Dozens of people will be doing that but its still pretty spooky/wierd/breathtaking to be on the grounds in moonlight.