If you do not run the ABS pump, you are not flushing the entire system. And you need a scan tool such as VCDS to do that.
What I do:
Remove the fill cap, and remove the filter screen and clean it thoroughly. Then dry it with air. Then snap it back in place. Then I open all 4 bleeders, leave the reservoir cap off, and let it gravity bleed about .5 L through. I like to use the Ate blue and yellow fluids alternately for the color change so I know it has been drawn through. I have an air-powered brake bleeder device that can speed this process up, but I generally only use that for pulling fluid through a system that has been dry (such as after a master cylinder or ABS pump module replacement). This is a good time to do some other services while you slowly add fluid. You do not want to let the reservoir go empty!
Once I get the fluid through, and I see a clearly different color fluid at all 4 corners, I close the bleeders, top the reservoir up, and put the cap back in place.
Then I grab the laptop, and access the ABS controller. I first do the <output test>, while sitting in the driver's seat, and go through and do exactly as it says, depressing and releasing the brake pedal. You only need pause for about 1 second during each mode. This only takes about 2 minutes tops.
I then do the gravity bleed bit some more, maybe another 5 minutes or so. Top the reservoir again, replace the cap.
Then use the VCDS again, and go into <basic settings> Group 001, and then pump the brake pedal about 10 times. Stop, repeat, stop, repeat. Then open all the bleeders again, with the cap off, draw that last bit of fluid through.
Then after it is all together, as I drive out of the shop, I do the <output test> sequence once more.
This is the procedure I use for PM fluid flushing, NOT for bleeding for a new component install. This gets all the fluid flushed out of not only the service brakes but the ABS as well. You also excercise all the ABS components that may not get worked under normal driving, and pushes any old fluid out of the ABS pump and valves into the system to get pushed through.