Open the scenario file in any text editor. Below is the first portion of the file from the Revolutionary War scenario. You put the "Victory=..." lines in for the ones you want enabled. However, if no victory conditions are listed, it means that all are enabled.
Version=11
BeginGame
Speed=GAMESPEED_NORMAL
Calendar=CALENDAR_MONTHS
Option=GAMEOPTION_NO_CITY_RAZING
Option=GAMEOPTION_NO_CITY_FLIPPING
Option=GAMEOPTION_FLIPPING_AFTER_CONQUEST
Victory=VICTORY_TIME
Victory=VICTORY_CONQUEST
Victory=VICTORY_DOMINATION
GameTurn=6
MaxTurns=100
TargetScore=165
StartYear=1775
Description=TXT_KEY_AMREV_DESCRIPTION
ModPath=Mods\American Revolution\
EndGame
I believe the others not listed in the above example are VICTORY_SPACERACE, VICTORY_CULTURE and VICTORY_DIPLOMATIC.
Also, you can create a Custom Game with the rules settings you want, start the game, then switch to the world builder and save. The resulting scenario will have the settings you want.