well I don't know 3SGE engines but I do have a rough idea how Toyota do things.
top pipe: definately the water bypass pipe. This circulates hot water when the engine is cold and the thermostat is closed. Getting rid of this will mean that the water will be stagnant inside the block till it heats up. Although far from idea many people have done this without an issue. Some drill a few small holes in the thermostat to keep the water going.
bottom pipe: water outlet very likely going straight to the heater core. Going to run a heater?