Gatekeeper, as has been discussed above, is a general purpose anti-virus utility which knows little or nothing about specific viruses. It stops viruses from operating by carefully monitoring your Mac and stopping any suspicious behavior that occurs. It has been remarkably successful in stopping both the viruses that existed when it was first released and those that have appeared in the years since then, but no anti-virus system can ever be perfect, and at least one virus appeared that could get around Gatekeeper's protections. That's why Gatekeeper Aid exists.
Gatekeeper Aid is a utility that searches for and removes families of known viruses which Gatekeeper either can't stop at all, or can't stop completely enough to render harmless. Over time, its role has been expanded to include some general purpose anti-virus duties as well as the detection and removal of some viruses that Gatekeeper can stop successfully, but which also happen to be easily detected and removed.
Together, Gatekeeper and Gatekeeper Aid form a security system capable of stopping all known viruses, and one with a proven (if inevitably imperfect) ability to stop new viruses as they appear. This is why it's crucial to use both products; one or the other isn't enough to provide effective protection.
In spite of this, it is possible to use Gatekeeper Aid independent of Gatekeeper. Some people use Gatekeeper Aid to augment the abilities of other anti-virus utilities, like the Disinfectant INIT. Rest assured that 'Aid still works perfectly well in such setups.