What is the best way to keep everything organized and spend less time setting up?
For card selection, I highly recommend the iDominion iPhone app.  Lets you specify which sets to include, blacklist individual cards, require Reactions if there are Attacks, and even re-roll one card of the 10 if you just hate the Smithy.  There's also a "lite" free version.

I have all of my cards (Dominion, Intrigue, Seaside, and Alchemy) in two collectible-card-game "long boxes", sorted by set and by name.  (Mine are sleeved as well, but that's not required).  Use one of the many dividers on BoardGameGeek to assist in locating cards.

It's easy to have one person take each box and pull out the cards you need, and for others to chip in parceling out the gold, VPs and starting decks as they're pulled from the boxes.

You can divide up the work this way with the original boxes, but card boxes take up a LOT less table space and the ordering of cards in the original boxes can be highly confusing.