Secure the frame and rear wheel simultaneously by locking the rear tire through the rear triangle. See http://www.sheldonbrown.com/lock-strategy.html

Remove the front tire and include it in the lock, too. Or, just wrap a cable around the front tire, and attach it to the rear lock as well.

If the lock is too big, you provide leverage for thieves, or something like that. A Kryptonite Mini is usually just big enough to lock up one wheel; use the larger locks if you are going to remove the front wheel, too.

I have never seen a good solution for securing a seat and seat post.

Total bike security is impossible, unless you are lucky enough to have a bike locker. You can probably secure your frame and your wheels, but that won't stop a thief with an allen wrench from removing other valuable components, like brake calipers or derailleurs. So, save the Dura-Ace bike for the weekend rides, and ride on a modest, practical commuter that doesn't have expensive components.