I'll just say it before I loose all patince. Make a sector, make the floor -100 and the celing 600 and then make a sector around that. Give it a floor of 0 and a celing of 600. Then click the middle sector in sector mode and find "Setup FOF". Click it and make it a water type, set the bottom height to -100 and the top height to -5. Then click ok. You have a pool of water.
Edit: This is in SRB2 Doom Builder.