I'm a little confused here.

How do I merge the new Scum and Villany cards with the original decks?

Do I use the new phase card or the original phase card?

Do I just throw all the new unit and event cards in with the original deck that I was using?

Why are there double objectives?

You can build your deck following the rules and guidelines stated on P.28 of the rulebook in the Core Set.

There is two because you can have two objective sets that are the same per deck unless the objective states otherwise.