Way too much there to even sum up, but I'll try.
The clone troopers were commissioned by Darth Tyranus/Count Dooku, under orders from Darth Sidious/Palpatine to serve as the Grand Army of The Republic. This action was widely accepted by the populace due to rising tensions from the Separatist Movement, also orchestrated by Palpatine. The entire objective of the Clone Wars was to spread the Jedi thin across the galaxy, and surround them with the clone troopers. Once Order 66 was given, the clones would turn on the Jedi in their midst and kill them. Since the clones were just following orders, the Jedi would not perceive any malice or ill intent through the Force. The Clone Wars were, start to finish, intended to be nothing more than the perfect Jedi trap. Most of the Jedi that survived were subsequently hunted down in The Great Jedi Purge.
As to why the clones wear armor resembling that of storm troopers, this can be seen as Lucas drawing parallels to his original trilogy. This happens frequently throughout the prequil trilogy, such as Darth Maul's fighter superficially resembling a TIE fighter.
Darth Bane was responsible for creating the Rule of Two (i.e. - one master, one apprentice.) Prior to this, there were many Sith of varying factions throughout the millennia. The faction at the the time of Bane's rise to power was known as the Brotherhood of the Sith. Ultimately, Bane became disillusioned with the power-mongering and infighting within the Brotherhood, and almost single-handedly brought about its' downfall. Henceforth, Bane decided that there would be only two Sith at any given time, "One to embody power, and the other to crave it." Apprentices generally killed their masters when they had learned all they could from them. This continued for thousands of years, with each generation of Sith building upon the groundwork that ultimately culminated in Episode 3, with the (almost,) complete destruction of the Jedi, the fall of the Republic, and the rise of the Empire.
The "un-dark" side of the Force has frequently been refered to as the Light Side in Expanded Universe writings.
Whew. That was fun. . .
