[pgermond]

I'm assuming from your post that you have one MC that supplies the front and rear brakes (is that accurate?). That being said, one should start the process with the brake cylinder or caliper furthest from the MC and work your way to the one closest. You didn't specify what type of brakes - some disc brake calipers have multiple bleed valves (i.e. Wilwood) you should use the ones on top for bleeding. This allows the caliper to fill completely.