Multiverse Theory is a range of theoretical attempts to impose a structure on the known characteristics of the Multiverses. It is, of course, untestable by any normal beings, and the Flowers aren't telling. This technically makes it a set of hypotheses rather than theories, but who cares?
The Underlying TheoryEdit
Put briefly, the basis of the Theories runs like this: a world will usually consist of three spatial dimensions (height, width, and depth), and one temporal (time). In most cases, the world is locked into moving on a determined vector along the temporal dimension, while moving freely in the spatial ones. Multiverse Theory states that there are in fact three temporal dimensions, to match the three spatial ones. One, the observed one, is time as we know it, or depth-time. The other two, commonly rendered height-time and width-time, are not observable by normal spatial beings, as they are incapable of moving in them, and (this is important) do not have a constant motion in them, unlike depth-time.
Two Multiverse TheoryEdit
The Two Multiverse version of the theory states that width-time consists of innumerable Alternate Universes based on the continuum one occupies at the time. This may be identical with the fifth dimension named "probability" by the Flowers, or it may not. Height-time provides access to the different continuua -- in other words, moving time-up may move you from Lord of the Rings to Harry Potter, while moving time-right will take you from a Legomance into a slashfic.
It is unclear where the Mirror Multiverse falls in this theory. Some claim it is a separate Multiverse in its own right, where everything started off reversed (as opposed to the normal Multiverse, in which all variations started identically but split off at various points). Others say that the extreme time-left of the Prime Multiverse is identical with the extreme time-right of the Mirror Multiverse, and thus that they are merely widely separated sections of a single Multiverse. To test this theory would require a great deal of time and expense, and the use of PPC portal technology; thus far, the Flowers have not granted permission for this to occur.
The Two Multiverse theory explains clearly why PPC Agents are able to travel between various fictional worlds, and across variations on them. It also makes the Mirror Multiverse unique, and thus transfers between it and the Prime Multiverse a Big Deal.
The main weakness of the Two Multiverse theory is that it makes travel between alternate versions of the PPC as easy as travel between fanfics, which is manifestly not the case.
Many Multiverse TheoryEdit
The Many Multiverse variant on Multiverse Theory says that both height-time and width-time transfer a person to different continuua. Alternate universes constitute different multiverses -- thus the Prime Multiverse and Mirror Multiverse are merely two among many.
The Many Multiverse theory explains why alternate versions of the PPC do not often interact with the Prime version -- they are not only separate universes, but separate multiverses. It also makes the distinction between Prime and Mirror Multiverses clear, while in the Two Multiverse version, there is some confusion over how they are separated.
If fanfiction creates alternate universes of fictional realms, the Many Multiverse theory would place them in alternate multiverses. This would make travelling to them nigh-impossible using PPC technology, which is patently not the case.
Travel within a multiverse is possible by many means, including of course PPC portal technology. However, travelling between multiverses is much harder. A malfunctioning TARDIS may land its operater in an alternate universe (as in the Rise of the Cybermen and Inferno episodes of Doctor Who), although whether this constitutes crossing multiverses depends on the theory you subscribe to (Two Multiverse theory would cast Rise of the Cybermen as part of the Prime Multiverse, with Inferno perhaps being a manifestation of the Mirror Multiverse; Many Multiverse theory paints them as separate multiverses). Unambigumous travel between multiverses is less common; the best known occurances occur by accident, as did the Inferno trip for the Doctor. However, it appears that Mirror Makes-Things succeeded in developing a machine that can travel between multiverses at will.
"Imagine, for an instant, that a storyline is just that - literally a line, stretching through some meta-space. It's been Published, which makes it extra shiny and special. That storyline is the Canon for that particular work - Lord of the Rings has a Canon (two, if you count the movies), MIB has a Canon, and so on.
Immediately surrounding Canon is a tight weave of well-written fanfic storylines. It's like a rope - all nicely aligned, woven together, and although parallel threads don't always agree, the whole thing holds together nicely. This is good fanfic. Each fanfic takes a little bit of strength from the main Canon, but because it weaves right back in, the net effect is to make the whole thing stronger.
Surrounding that is the whole tangled mess of badfic, which makes our nice, neatly woven rope of fandom look like a messy yarn-ball. It's ugly, it's messy, and as each fic still takes strength from the Canon, it weakens the entire assemblage. The job of the PPC is to trim out those tangles and keep the rope of canon something resembling coherent and linear."