Due to the presence of Kevin J. Anderson in writing Frank Herbert's son's extensions of the original series, you just can't compare them. If you read the father's series first, and like it, then you'll enjoy the extended series for the "Dune universe", but I can almost guarantee that you'll hate what that hack Anderson did to it.
SPOILER ALERT! SPOILERS FOLLOW!
The Dune universe as published by the father only covered about 6000 to 8000 years of time, from the era of Muad'dib (Paul Atreides), down to the continuance of the Atreides line through people like Miles Teg, Darwi Odrade, and Sheeana ... as well as the ancient cells of the Atreides remaining in the possession of the last Tleilaxu.
HOWEVER, Anderson's hackery with Frank's son produced another, enveloping storyline, based upon a singular entity (i.e. that old "Dark Lord" meme that hack authors love to rely on) called Omnius (
http://en.wikipedia.org/wiki/Omnius), against which the Butlerian Jihad was allegedly waged. Herbert's son claims that Omnius is based upon his father's notes, but the entire concept from soup to nuts is so filled with hack that it actually seems to be a creation of Anderson (who as I've pointed out, IS a hack). Anderson managed to start the early Dune books based upon this Omnius crap, and then managed to bring it back to be the Big Bad Guy for the next book following where Frank left off (in "Chapterhouse: Dune"). Omnius Omnius Omnius -- fuck, Kevin J. Anderson has got fucking Omnius ON THE BRAIN!
Look, just do yourself a favor, and stick to the "class Dune", to wit:
http://www.dunenovels.com/classic.html