I just went through this process myself on our car with the brakes and the clutch. Here's what worked for me, starting with brand new (ie dry) MC's out of the box:
I mounted the MC's and then bench bled them by making short tubes that routed fluid each MC back to its reservoir. For each MC, after pumping the pedal slowly about 20 times, I filled the reservoir up, disconnected the bench bleeding tube I made and reconnected the brake line to the MC. Watch where the fluid leaks if your car is painted
. Mine's not, so it wasn't a big issue.
Next, I used a vacuum bleeder, as Bob and Roscoe suggested, to pull the fluid through the system. Be patient and work slowly. I started at the pass rear, then the drv rear, pass front and finished up with the drv front, as usual. Repeated this about three times and the pedal is very firm. HOWEVER, it was difficult to tell when all the air was out while bleeding because the bleeders like to pull air around the threads on the bleeders. After removing the bleeders and giving them a light coat of anti-seize, this problem is fixed and the vacuum bleeding method really works great. The anti-seize is a good idea anyway, as they will eventually cause problems otherwise.
As for the clutch, I couldn't get any fluid to pump out of the MC until I pumped the pedal quite quickly a number of times. Later I read this is the way to begin bleeding a clutch. Once the fluid begins to exit the MC (assuming the line and slave are below the MC), the clutch will gravity bleed itself very well. I finished up with the vacuum bleeder because I was impatient and everything took a little over an hour.
And as always, watch the level of the fluid in the MC's or you'll have to start over
. Also, be sure to check for leaks once you begin checking the pedal...
Mike