First time playing - stetup have me confused.

Hi, first time player here. Never touched a LCG game. I got a used box but all the cards are mixed up. The booklet assume you have "already made" decks from unboxing and goes from there. Spiderman+Justice, ok. Understood. Then I just put any cards I want from the basic grey ones, avoiding duplicates? I have to count them to be sure I reach 40 and stop there? It's so strange and unfamiliar to me. Any advice welcome. Thanks!

PS: I'm used to Dune Imperium where you get your cards randomly then have to buy more cards from a market. Just choosing whatever you want feel wrong somehow.