So I got the game on pre-order, and in my GOG library it says +3 DLC, and I have 2 DLC files(assuming "DLC: Pillars of Eternity: Pre-Order Bonus Item and Pet" is considered as 2 items/DLC?)

Anyway when downloading them i get .bin files. Where do i need to put them to get those items in game?

I bought the champion edition, with that I got two 2 DLC items, Almanac and Pet. I have downloaded setup executable, 2 binary files + the setup DLC.executable. I first installed the game, then run the DLC executable...that's it and it works fine.

I do have issue which I'm trying to sort out with gog support, I have whole bunch of binary files on my game page that are 1MB big and i can't download them. However, I do know installing the DLC executable worked because I have the Pet (piglet) in the game working just fine.

As BlackJaguar said, you don't need to worry about those .bin files, just launch the executable and let it do its thing, then apply DLC .exes.

Concerning the DLC (might want to make a sticky considering how often the question appear on these forums), you need to meet the proper conditions :

DLC 1 : preorder item + pet, for everyone who preordered (duh)
DLC 2 : KS item, for every backer
DLC 3 : KS pet, for backers with a 50$+ pledge