The best place to put the pump is just before the RO unit. On the RO unit, the bottom three cannisters are, from right to left:
Sediment Filter
Carbon Block
Granular Activated Carbon
These three take out the nasties that would damage the RO membrane. The top membrane unit then works on a reverse osmosis principle, only allowing clean water molecules through. As the dirt builds up on this membrane it needs to be flushed off regularly. To do this, open up the flush valve to allow most of the water freely passed the membrane surface and out the waste. I would do this for about 3-5 minutes before each major tank fill.