Congratulations on your epic purchase!
Personally, I have organised my cards by expansion in a binder, as I like leafing through them and seeing how the game has grown.
However, my cousin organises his cards by Card type (dudes, deeds, actions, goods and then each spell type separately), then within that by faction (for dudes) then value. From experience building decks together, this makes putting decks together much faster. He uses boxes for this - not as easy to see things as a binder, but a bit faster to look through.
Both options can work well, a bit of an aesthetics v efficiency tradeoff between the two options we've gone for. 
