Hi Chris,
The two main drains are connected and one line is connected with a "t" and runs back to the equipment. The reason for two main drains is anti-entrapmentn protection.
The reason return lines are 1-1/2" through the wall is because the inlet eyeball fitting is made to fit into it. The main return line will depend on the factors I mentioned before, but usually 1-1/2" or 2".
Looking to the future... if you are thinking of getting a heater later on, the plumber can do a heater stub-out. You can do the electic to the heater also, but it will be extra.
Not all Polaris cleaners require a booster pump. I believe there is 280, 360, 380, and 480. You can check them all out on www.polarispool.com.
There are also suction side cleaners such as a Hayward Navigator. (Polaris is a pressure side cleaner).
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