It's the newly placed monsters you're distributing evenly. The "they" in that sentence refers to the monsters you're placing.
So you're mostly right about your example: to place six monsters on three gates, you add two to each, no matter what was already there.
But remember, the monster limit is the number of players in the game plus three. Presumably if a monster surge makes you place six monsters on three gates, you have six players, so the monster limit is 9. If there are already 5 monsters on the board, you can only add four more, and the last two will go to the outskirts.
The Arkham Horror FAQ clarify that situation a bit:
When placing monsters, they must be divided as evenly as possible among the open gates, with no gate having more monsters placed on it than the gate where the monster surge occurred this turn.
So in that example, you'd place two on the gate that caused the surge, one on each of the others, and two in the outskirts.