Why is charge of the electron negative? How did scientists figure out that the charge of the electron was indeed negative? I know how the cathode ray tube experiment works, but how did Thompson know that the plate that the cathode ray beam was attracted to was positive, meaning the cathode ray was negative? What is the history behind positive and negative charges leading up to the cathode ray experiment. Ben Franklin postulated that a body with excess electricity was positive as in a surplus of electricity, and that surplus flows from positive to negative. But how and when was it discovered that electricity flows from negative to positive? 
 A: Benjamin Franklin proposed electric fluid theory and considered electric current to be flow of a charged fluid.  He meant to use positive to denote a surplus of the fluid, negative as a deficit of it.  No one knows how he came up with the choice, but it became the convention and as a result lead also to the labeling of charge.  I know of no fact that could lead him to that choice.  It might just be random.  Years later Thompson discovered electron, and according to already established convention, it had a negative charge.
A: That there are two distinct types of electric charge is a metaphysical fact.  
But nature is indifferent to what we choose to label these charges; up / down, left / right, positive / negative, black / white, etc.
Electrons will still flow to the plate in a CRT regardless of how we choose to label the polarity of the charge on the electron and plate.

Regarding electricity, from the Wikipedia article "Electricity": 

Electricity is the set of physical phenomena associated with the
  presence and flow of electric charge. Electricity gives a wide variety
  of well-known effects, such as lightning, static electricity,
  electromagnetic induction and electrical current. In addition,
  electricity permits the creation and reception of electromagnetic
  radiation such as radio waves.

So, while we can meaningfully talk about, e.g., electron flow and charge flow, electricity flow is not particularly meaningful.
A: As Zeldredge said the name is arbitrary and does not matter electron could have been positive and protron negative just the name.
A: Answering the first part:  how was polarity first arrived at?
Simple:  electrostatics is part of electromagnetism in general, and the names of the charge polarities come from electrostatics history.
Fur touched against rubber becomes net-positive while the rubber becomes net-negative.  Early electrostatic voltmeters, the "Quadrant Electrometers," followed this standard.  These are voltmeters based on moving capacitor plates, and the ones with fixed polarity would use high-volt batteries to charge their pos. and neg. field plates.  To determine electric polarity, just check the +- using your electrometer bought from an 1800s science supply company.  Or fifty years later, the same standard was adopted when non-impulsive currents had been discovered and current meters were being sold.  You could check polarity with the d'Arsonval Galvanometer you'd bought.  The marked +- on an ammeter was determined by permanent magnet poles and the coil winding direction.
Actually it was Ben Franklin who assigned the "positive" label to the rubbed fur's charge, since earlier it had been called Vitreous.   (Rub glass against amber, and the "vitreous" glass becomes positive, while the "resinous" amber negative.)
For the Cathode Ray experiment, the positive plate would be connected to a positive terminal of a high-volt power supply.  To determine the polarity of your commercial power supply, just look at the colored terminals, or check it with your voltmeter.  To verify your voltmeter's polarity, compare it to another commercial voltmeter!  :)  Or, connect it to a zinc/copper/saltwater battery (where the zinc is always the negative plate.)  To verify that zinc battery-plates are the negative ones, use your voltmeter to discharge a capacitor where the capacitor dielectric is a sandwich: a layer of rubber and a layer of glass between adhesive metal plates:  touch them firmly together and separate, and the metal connected to the rubber side will charge up negative, the glass positive.  Now test the zinc-plate battery with your polarity-calibrated voltmeter.
Hint:  with just a piece of plastic and fur you can check your voltmeter.   In dry conditions rub the plastic on clean hair or wool.  Now ground your negative voltmeter lead, or connect it to a large conductive object.  Set it to the most sensitive voltage scale.  Now suddenly move the voltmeter's (+) probe towards the charged plastic surface.  If the meter polarity is correct, the meter will momentarily indicate a negative reading.  Yank it away again, and you'll see a positive reading.   By moving the meter lead suddenly towards a negative-charged object, you're capacitively attracting positive charge towards the end of the meter lead, and capacitively repelling negative charge into the meter's (+) connection, producing a negative reading.
Second:

But how and when was it discovered that electricity flows from negative to positive

It doesn't.
Believing that electrons equals electricity is a common widespread grade-school myth.  It's easily debunked:  in electrolyte conductors like battery-acid, the movable charge carriers, (the +H ions also called protons,) flow in the positive direction, while outside the acid, the electron clouds within the metal plates flow in the negative direction.  And in salt water the "electricity" always has two polarities: negative chloride ions and positive sodium ions.
That means that in oceans, and dirt, and in human tissue, the electric current is two separate currents, positive and negative carriers, flowing in opposite directions in the same material.   'Poor Richard' was wrong.
The Cathode Ray Tube experiment demonstrates electron beams, but K12 textbooks usually don't mention the other one, the "Canal Ray" tube with its violet beam coming out of the positive electrodes.  This tube showed the mysterious positive current made from massive particles barely deflected by a magnet.  They were high-speed positive air ions; the positive part of the electric current found in any plasma.
Besides flawed grade-school textbooks, another big source of the misconception was Navy training manuals from WWII, where apparently all proton flows were carefully avoided.  Perhaps they were too confusing for rapid "emergency training" of hoards of repair  technicians?  Instead the military students were only taught about vacuum tubes and metal wires, the conductors where the only mobile "electricity" were clouds of electrons.  With this warped view of basic physics, it's no wonder that entire generations would believe that Electricity is made of Electrons, period, and that currents made of flowing protons cannot exist.  Yet when you zap yourself, no electrons flow through your body.   You're not made of metal, after all.
