When I actually set up the tubing, I changed the routing slightly and took out both hard drive cages. The pump feeds into the rear Phobya inlet, out to the CPU block, from the block into the front EX240 inlet, out the rear inlet straight down into the reservoir. I did the fill and drain tubes as depicted above.
The pump I wound up suspending in the air about an inch from the case bottom, and "anchored" with 3 velcro strips. This is pump mounting seems to make it very quiet.
After playing around with different mounting ideas for the Phobya, I did wind up going inlets down, and leaving enough clearance at the top for the bleed screw to be used with needle noses. FYI, I'm using a 180 mm Silverstone AP-181 fan using the Phobya adaptor plate, with the fan in a pull. I used the other adapter plate on the other side of the radiator.
I did this to give me a bit more surface area at the corners, and used velcro there. I filled in between the velcro on all sides with some narrow and thin foam insulation tape. Then trimmed up to give it the full airflow area of the plate. Then just aligned and stuck it to the front of the case. Seems to work fine, and should give a bit of decoupling and seal.
I liked the use of velcro because the fan/radiator will come out easily for cleaning. The only other thing I'm considering is getting an additional filter - one of those magnetic ones stick on type to put on the exterior side of the mesh cutout to keep the radiator cleaner than the stock filtering might provide (it's setup as intake).
An alternate method I almost used:
The adapter plate does have holes that align with the stock fan holes on the case. That would be great except for the bleed screw which just bangs into the bottom of the drive bays, and keeps it from lining up.
If you don't mind some drilling/filing on that drive bay bottom, you could make a hole for it to go through, and have easy access to it as well from the bay space above.
This is all IF you are using a 650D case, BTW.
I just finished filling the loop and started the leak testing. It took slightly less than a liter to fill. So far so good, as the optimistic who fell from a 50 story roof top yelled as he plummeted past a 25th story window.