Item splitting is a bit less elegant with Redpower than with Buildcraft, because tubes have different behavior than pipes, and there's no equivalent to the distribution pipe. You basically have to implement the splitting in the machines instead of in the pipes.
Have the Quarry output (or at least the cobble) arrive in a chest. Place a sorting machine next to the chest. Remember that it needs Blutricity - when you're outside, placing a solar panel next to the sorter will do, but inside you'll have to build a thermopile or run blue alloy wire through the nearest wall. Also build a timer and place it facing the sorting machine.
Leave the sorter in sequential mode (the default). Specify a different color in the first three slots. Place 4 cobblestone in each of the first three slots. Connect pneumatic tubes on the output side and make a 3-way fork. Create some paint in the colors you selected inside the sorter and paint each of the three tubes a different color. Those tubes can now lead to your three different destinations (cobblestone storage, stone making, and brick making).
What will happen is that the sorting machine will send packets of 4 cobblestone first down the first tube, then down the second tube, then down the third tube. If there is not enough cobblestone to make a full packet of 4, it will wait until there is enough. Afterwards it will repeat the pattern. If you need to make it faster, you can a.) increase the speed of the timer or b.) increase the packet size (sending 16 cobblestone instead of 4 for example).