I'm not en expert in water cooling either, but I can answer some of your questions.
Cooling them in series, according to my understanding, would not be very effective as the last waterblock would have warm coolant flowing thru it. Can I split the line into three smaller lines and run them through the waterblocks in parallel, rejoining them before entering the radiator? Or is there a better way?
Definitely not true, or they wouldn't sell those nifty little kits to easily place GPU water blocks in series. The temperature of the coolant isn't the important part. Although its generally assumed that keeping the CPU and GPU loops separate, or at least on separate sides of the radiator, most of the time it doesn't matter. It's more simple than you make it seem. The important part of a cooling system is that it absorbs Calories from the heat source and dissipates them by radiating them into the surrounding air or some other kind of output for the heat. Since water has a high specific heat, running through other water blocks won't change the temperature of the water enough to disrupt this pattern in subsequent blocks.
In other words, you'll be fine with one continuous loop.
And when leak testing, I read to run the pump with the computer off and everything installed for 12 hours. When you do this, are you sitting there watching it for 12 hours straight? It sounds mind numbing, but I don't know how else you would react quickly enough to leaks... How does that work?
No, you don't want to install the water loop into the system before leak testing, because if it leaks it will still get on the computer, defeating the purpose of leak testing. Build the loop outside of the computer with the blocks not installed, hook the pump up to the PSU, fire up the PSU, and run the water through the tubes for the required time in a place where any leaking water won't damage anything. Once you're sure it isn't leaking, install the blocks.