So in these situations how do you tell apart electrons from one source compared to another? In the article they mention how the LHC collides particles at a rate of "40 million times each second". I can imagine there are a lot of electrons and other particles flying around from other collisions. What makes an electron discernible between one type of particle and another?
The point is, we cannot tell which pair of electrons/muons come from the decay of a specific particle, but we can tell how many extra occurred beyond what we would expect from all other known processes.
If you don't mind my asking, what are you doing now after spending years studying such a specific area of particle physics?
Some of the best data for branching ratios comes from e+e- (electon-positron) colliders such as LEP (literally, the Large Electron-Positron collider). In these colliders, we can fine-tune the energy to produce massive amounts of particles we care about. From that, we can see how they decay. Mostly, Upsilons decay into massive sprays of hadrons and leptons (called jets in particle physics). These can come from decaying Tau particles (the much much heavier cousins of muons and electons) or from quarks/hadrons decaying over and over and over again into things like Kaons, pions, muons, electrons, photons, and other lightish particles. In the relatively clean environment of a e+e- collider, we can reconstruct these jets and determine which may have come from Upsilons. Combining this with a whole bunch of other measurements (and some theory) lets us determine the branching ratio (how often a particle decays into certain things).
The scattering matrix is calculated by including all the possible interactions you expect. So a matrix including some intermediate C will be different from one that does not.
Then you can line up what you actually observe and select the matrix that most accurately describes it.
The extra path does not necessarily raise the probability. The interactions are more complex than that. The simplest thing to say is that it affects the distribution.
It's 511 keV at rest, and you are sensing a 4.73 GeV electron coming out of the decaying Upsilon. E=m and c=1 in the units you are using.