In the “build you custom deck mode” each player has to prepare a deck before the game starts (like in trading card games like MTG or Hearthstone). The game plays like a standard “IT Startup – The Card Game” game: the only difference is where you draw your cards from, and where used up cards go. Instead of drawing from a shared deck: each player draws from their own pre-build deck.
You may pick your own deck building restrictions. For example: the deck must contain at least 32 cards and only 2 copies of a single card are allowed. The only important thing is that each player builds their deck with the same deck restrictions.
Important note: to properly build your custom deck each player must have access to the same card pool. You may also mix things up and build your decks in a draft- like format.