From the Condition Setup help handout:
Condition Menu
Name — The name of the condition Type — Determines if a Spell or Condition. Set to spell if using concentration Icon Type — Determines what options are presented when clicking Icon . CombatMaster — Lets you pick from Roll20 default markers only. TokenMarker — Requires the libTokenMarker script; lets you pick from any marker sets in your game, including Roll20 default. NOTE: Token marker names with spaces may cause issues, it is recommended to avoid spaces in token marker names. TokenCondition — Requires the TokenCondition script; lets you pick from any characters used by this script. So add the libTokenMarker script from one-click to your game (you may need to wait a while and/or reset your API a few times before it registers all your custom markers). Then from the Condition Setup menu, change Icon Type to TokenMarker. Then you can change Icon to a marker from your custom library. You'll need to do this for each condition that's gonna use a custom marker.