Didn't a massive Sith army battle a Massive Jedi army on the planet Russan and that was the last encounter any Jedi had with a Sith until Qui-Gon and Obi-wan?

If so then how did Yoda know only two there always will be?

Didn't a massive Sith army battle a Massive Jedi army on the planet Russan and that was the last encounter any Jedi had with a Sith until Qui-Gon and Obi-wan?

 

If so then how did Yoda know only two there always will be?

You're referring to the Bane Trilogy. Also in the Trilogy, Bane makes a point to allow a few unscrupulous types know, or at least think they know, of living Sith's existence.

Those rumors eventually made it back to the Jedi.

"In the article "Evil Never Dies: The Sith Dynasties," Abel Pena came up with the explanation that a Sith cultist named Kibh Jeen (introduced in The Living Force Campaign Guide) had spilled the beans about the Sith, but was a raving lunatic whose testimony could be dismissed by any skeptical Jedi."

―Daniel Wallace

http://starwars.wikia.com/wiki/Kibh_Jeen

Not the most satisfying of plot-hole fillers ever to grace the Star Wars Universe, but its what they're going with.

I figure that, through the Force, some of the Jedi (including Yoda) were able to perceive the truth of Jeen's words, which is why he speaks about the Rule of Two as a known fact.