The Prime Multiverse is, for practical purposes, the multiverse that contains the PPC. It is also presumably the multiverse that contains World One and the majority of the continua that the PPC works in. It is, rather inevitably, part of the perpetual debate that comprises Multiverse Theory.
Within the Prime Multiverse there are also just as many scraps of failed continua and half-formed junk. Mostly this is avoided by the PPC, but a great many agents come from unpublished, never-finished, or discarded works of fiction.
There are many continua that highly resemble each other, but they are not the same and may or may not include the same people. A canon universe, no matter how similar to another one it is, is not the same as an alternate universe, and must never be confused with one.
A common type of similarity between continua is the tendency for creation of World One variants, such as NCIS or Stargate. Almost every continuum that has humans will also have an Earth, and the adventures of main characters will often take place on Earth. However, the World One variants are no more the same universe than any other two continua would be, despite how frequently multiple World One variants are crossed over.
When the very fabric of the PPC's nature is different in such a way that repercussions of such an alteration would be felt throughout many worlds, a new multiverse is formed. The PPC has made little contact with the the majority of these alternate multiverses, but a few have revealed themselves in minor ways, often involving a few entities from one multiverse passing through to another. One such trans-multiversal being is Agent Luxury, who was born in an alternate multiverse often called the Shipverse, and was transported to the Prime Multiverse's World One following an incident with a malfunctioning Remote Activator. The PPC has made no further contact with Luxury's home multiverse, which, given that Luxury's behavior seems to be the standard there, is probably for the best.
Several other versions of the multiverse are known to exist, including the Arthurverse, the Sundering Alternate Multiverse, and the dramatically named Mirror Multiverse. The latter is the only one that has tried and succeeded to deliberately contact the Prime Multiverse thus far, though the Sundering Alternate Multiverse has had contacted it by accident in two brief but crucial intersections, the first occurring as part of the attempted temporal transport of Jasmine Sims by the Ghost in the Machine, and the second occurring as a complete accident involving the post-Sundering instability of portal technology. However, the second intersection was what caused the split between the two multiverses in the first place by pollinating the Prime Multiverse with news and technology of the Sundering multiverse, which had been, from the perspective of those displaced, at a period of time seventy years in the Prime Multiverse's future. This goes to show that the Prime Multiverse, despite its name implying a high position over other multiverses, is simply one of many possible timestreams that are not necessarily mutually exclusive.