Your lowest tier troop gets selected to gather regular nodes. We have requested this be changed a couple times. However, this is ''fixed" for raids. For raids, the troop with the fastest gather speed gets selected first.
If you kill off all militia and guards it selects hunts for you. It's a good idea to kill them off when you get enough t3 troops anyway, or when you get attacked your hospital fills with the lowest tier troops first and you lose your t3 troops.