I found the best way to do it is also the hardest way (like everything in life).
I first install all of the waterblocks and components exactly how they will be during operation. I then cut out all the tubing so that it is the proper length. Then I remove the waterblocks and components from the PC. Next I attach all the tubing and fill it. It is a lot easier to fill outside of the system. Once it is full of water (all the air is out), do a leak check for 30 minutes - 24 hours. Then install into the system, do another 5 minute leak check, and off you go.