I've just recently come back from dissecting my printer to replace the dampers. While I was in there, I pulled out the capping station and studied it. Hopefully this information will be enlightening.
There are 2 lines leading from each pad: One large and one small.
The large lines go into the capping station pump, which from reading the manual, uses rollers to roll along the tube, creating the pumping action. These lines go directly to the waste tank.
The two small lines go into another area of the capping station system, but I cannot figure out where without pulling the entire thing apart. I believe it is these small lines that drain the capping station normally. Since they are small-gauge, they could easily become blocked with crud.
It is assumed, since a drain cannot be found, that they somehow join into the large lines inside the pump, probably directly after it.
The very obvious gear can be turned "right" to unlock the print head. Continue turning it to move the wiper blade into the "active" position. Continuing to turn does nothing.
Turning it "left" will retract the wiper, raise the capping station, and then being pumping. You can use this to move flush through the large lines.
I'm hoping to be able to modify the capping station to work with an external waste tank, or a modified regular one that won't require absorbent material, but also won't spill.