The Clone Wars era, from 22 BBY to 19 BBY, is a period in time in which the Galactic Republic (DICE's version) and the Confederacy of Independent Systems (DICE's version) were at war. The Galactic Republic fought with an army made entirely out of clones (apart from the Jedi generals that led them,) constructed from Jango Fett's DNA, hence the war's name. The CIS (or Confederacy of Independent Systems) fought with factory produced Battle Droids. The war finally ended when Emperor Palpatine had all of the Jedi executed, and the droid army was deactivated.
Certain maps only have the Clone Wars era available, while others have both the Clone Wars and the Galactic Civil War. You will only be allowed to side with either the Republic or the CIS while playing the during the Clone Wars era. The only exception to this is Assault on Mos Eisley. The Clone Wars takes place during the Rise of The Empire Era. This era takes place between; but also includes; the Battle of Geonosis and the Battle over Coruscant; seen in Episodes II and III respectively.