This is a site with pics that I found fast searching + bleeding a mastercylinder.
Your Mastercylinder does not look like his but the Idea with the tubing is the same with the exception that most people stic the tubes in the Brake fluid Resivoir.
The main idea is to keep the ends of the tubes under the Brake Fluid so Air does not get sucked back in through the tubes. Also you do not have to put it in a vice to do it. Just leave it on the attached.
Some Members have suggested having the Engine runing when pressing on the Brake Pedal during the Bleeding process to not stress the old Diaphragm in the Brake Booster.
http://www.tegger.com/hondafaq/mastercylinderreplace/benchbleeding.html
After that it is still a good idea to bleed all of the Brakes as you did previously to get out any random Air Bubbles and flush our any nasty old Fluid.