My 2 core sets and scenario packs came today. I should only use I set of chaos tokens and put the set from one of the core sets aside, right? Is it ok to put the other other tokens together?

Also just use player cards from one core can be put with the other play cards, but only one set of scenario cards used? Even if I'm playing with more then 2 players?

Correct. You only need to use one set of scenario cards when constructing the encounter decks and setting locations. I have two core sets and I only use the tokens from one set and am keeping the others stored away in case my daughter runs off with them.

If you plan on going with 3 or more players, you should definitely put all markers for damage, horror, resources and doom/clues together; otherwise it is possible to run out of markers.

Remember to use only one set of basic weaknesses also.

Don't worry too much about mixing up the tokens - each mission will show you which tokens to use.

The Chaos Tokens are not a concern because each scenario/campaign will tell you how many of each token to put in the chaos bag. Scenario, encounter and basic weakness cards are entirely redundant. The only thing you need a second core set for is the player cards. Either to give you more options for deck construction for 1-2 players or enough cards to play with 3-4 players.

As has been stated many times elsewhere, having a second set of encounter cards enables you to have all three scenarios built and ready without having to mix and match encounter sets. I must warn you, though, that this approach becomes rapidly more untenable the longer into Dunwich Legacy you continue!