plumbing rear intake coolant ports

I have an air gap intake and a water neck spacer that I've plumbed to from back ports. My question is do I want it to bypass thermostat meaning thermostat below spacer with plumbed lines or should I have thermostat above plumbed lines. Also have water ports on sides of heads between headers can I plumb off the water pump to these or are they like exits plumb to spacer? Benefits and other ways to plumb coolant..
Don't have overheating issues just want to move water around mor efficiently