Do you mean, for them to save the ship, they'd flood water into parts of the Stern, like the Electric Engines, Turbine Room, etc? Or do you mean the ballast which would keep Titanic steady in the water?There's a more detailed description of the pumps location and performance in this clip by Bill Saunder.
There were 5 ballast pumps (in blue) for moving water in compartments along the hull of the ship to correct the angle of the ship. Presumably the Engineers pumped water from the bow to the stern compartments in these tanks, but the amount would have been small in relation to the inflow. There were also 3 smaller bilge pumps (in red), which are used to remove water from the ship.
I'm not sure if the ballast pumps could be used as bilge pumps, but the latter were linked by a long pipe running the length of the ship. I recall one of the movies implied that the engineers rigged a flexible pipe from one of the pumps to remove some water from the flooded boiler rooms.
To get enough water into the Stern to balance the ship would have required flooding of compartments which contained electrical equipment. There was an emergency generator on D deck though.
When Boiler Room 6 first flooded, the pumps were barely keeping ahead of the water. As Walter Lord described, the air was full of steam, and the water was waist high, and the water was black with oil and grease.
I know nothing about her pump system, but I'll try to explain my understanding. I think they pumped the water out of the ship, out of the discharges. There was a discharge outside the Turbine Room on G-Deck.
I believe they worked on the pumps as long as they could, but after an hour and a half, and she was still sinking, I believe flooding the Aft sections wouldn't save the ship, but again, I know nothing about her pump system haha.
You should ask Capt. Jim Currie or Sam Halpern. Those two men have worked on ships and know Titanic and her machinery like the back of their hands.
Hope this helps