The beginning level of Doom is specified on the Ancient One's sheet. Any card or effect that says to "advance" Doom subtracts that number from the level of Doom, and any effect that "retreats" Doom adds that number.
After the Ancient One has awoken, advancing Doom will have a different effect than normal: The Final Mystery will explain what happens when Doom advances. Retreating Doom has no effect if the Ancient One awakens, unless the Final Mystery specifies it.
Any card or effect that says to advance Doom will increase the level of Doom. However, there are other ways to lower Doom within the game:
If the Omen rotates, and the new Omen shares a symbol with an open gate, advance the Doom by 1 for each Gate.
If an Investigator is defeated or devoured, advance the Doom by 1.
This always holds true unless a card effect specifically says not to advance the Doom when this occurs.