No, you should not remove the ball or modify the cartridge in any way when doing vacuum refills.
Basically, the way it works is you submerge any openings into the cartridge below the level of the ink supply. When you pull a vacuum on the ink and the submerged cartridge, all the air in the cartridge bubbles out through the ink. Now you have a vacuum inside the cartridge where the air used to be. When you release the vacuum, the air wants to go back into the cartridge where it was before, but the ink is in the way so it pushes the ink into the cartridge.
To see a full description, complete with videos, go to the nifty-stuff.com home page (you can use the link at the top of this page just below the banner), then click on the link called "All Articles" near the top of that page, and finally scroll to the bottom of the new page and click on the link called Vacuum Fill Canon Cartridges.