I typically bleed my brake fluid when I change out the pads. I will look in the MC reservoir to see how dirty it is. I stir up the grim at the bottom of the reservoir and use a turkey baster or tube and pull out as much fluid as I can; usually keeping just enough to cover the outlet hole. Then I bleed the caliper till the fluid goes clear. I am probably not flushing the entire system. You will notice that the fluid near the caliper is darker. Not sure exactly why. I have read that it is dirt getting back through the piston seals. Also read that it is due to the heating of the fluid by the pads/rotor/caliper and degrades and turns dark.