My Aqua-rite is plumbed just prior to the return. I think you want any bits filtered out so they don't clog up the electrolytic cells. I would put it in the deep end.... but I am not sure it would matter much if the pool is turned over at a regular rate. I am new to pools so I wouldn't base any decision on my advice.
Man, that's a giant pool!! If I were you, I'd just put two cells on it . . . one on each filter. Less use of one cell and that way you know you'll get the chlorine production you need and won't have to worry about cell life as much, and also, you won't have to run one filter longer than the other. I just think, with that size pool, two would be the way to go. AquaLogic? I think they'd advise 2 as well . . . What is your gallonage?