flushing the system is a similar process to bleeding but more complete. i don't think you're supposed to empty it all out b4 putting in new fluid. rather you put in new fluid and push the old fluid out. iirc it goes something like this :
1. open up the MC and scoop that old nasty fluid out (as much as u can). then dump some fresh fluid in there to the proper level.
2. then going in the proper order (farther from MC to closest), go to each wheel and bleed the brakes until you see clean fluid coming out. make sure the MC does NOT bottom out while you are doing this; add fresh fluid as the level goes down. otherwise u'll get air in the system.
there are plenty of links on the internet that have DIY brake flush faqs... i'm sure the FSM must have instructions too. anyway, here's one:
http://popularmechanics.com/automoti...sh/index.phtml