I am curious whats the best way to route the waterlines to the e-top header's 3 water ports?

Not sure exactly what you mean???? It also depends on what Tstat housing you have and whether you have the 2 or 4 outlets on it.

Im not sure how to put a pic on here. But my thermostat has two ports coming out of it and one coming out of the crossover.

The port on the crossover is the in water from the sea water pump. The 2 outlets on the "T" stat housing each run to the collection tube running under the header tubes. You can plug the rear end of the collection tube or run it to a dump tube that will drain down your pipes after the engines are shut down.

and then install a pipe plugs in the upper hole at the top bend of the header.

I'm not running a crossover, but the way mine are plumbed is the same.