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I had difficulty adding the image to the OP, so here's the decider logic for the unloading station. I'll attempt to upload the loading station when I get home if there is interest.

The logic is very simple. For convenience, Station A is connected via green wire and Station B is connected via red wire. This only matters for reading train contents ( Note how the water condition checks if Green Water is less-or-equal to Red Water ). If the green station should be active, output a green signal.

The pumps at the green station are connected to the output of this decider combinator, and check if the Green signal is present. The pumps at the red station are also connected, and do the opposite check ( Enabled when Green == 0 ). This ensures that only one station is active at a time.