Their brains are removed and placed into the metal suit. When more soldiers were needed they converted the whole bodies to save time, this is what happened in the Torchwood story Cyberwoman. In "The Pandorica Opens" a whole skull was shown to be inside the helmet.
In contrast, the original Mondasian Cybermen from the classic series were the result of an almost complete replacement of human limbs, organs, etc., with cybernetic "spare" parts.
And the Cyber Legioners follow a similar strategy to the "Cyberwoman" example above, starting by inhibiting the emotions.