There "should" be precut little notches in the back of the hood for the output, input hoses. Input (from chiller) should go to final chamber where it returns to tank. Output (to chiller) will be best in like 2nd or 3rd, just not the same chamber!
What about having the intake (to chiller) in the 1st chamber and having the return (from chiller) in the 3rd chamber...would that work? I have a Maxijet 1200 as my return pump in the 3rd chamber of my BC29 and I have a Rio 6HF that I bought for my chiller's intake pump.
Yeah I would think that would be just fine. I have a Nano cube so I wasn't too sure about specific chambers so that should be GREAT! Do you even need two pumps on it? I only ask because on my chiller I have a MJ-900 in my second chamber and it is enough to push water from tank to chiller 2 feet down on floor back to tank UP two feet again with plenty of flow! I am not an expert by ANY means on chillers but I would think that if there is too fast of a flow through the chiller it wouldn't have enough time to chill the water.
My chiller recommends at least 300gph. I plan on having it sit on top of my fish cabinet next to my tank so it won't have a lot of head pressure to begin with. The Biocube comes with a return pump in chamber 3 that draws water through the intake grates in chamber 1 through the filtration system in the 1st and 2nd chambers and exits back into the tank in the 3rd chamber. The extra pump would be for the chiller only.