I've been fighting thrush with my four-month-old as well. For gentian violet, you're supposed to apply twice daily for at least three days. Use a Q-Tip, dip it in the gentian violet, squeeze out all excess and then paint the entire inside of mouth. Also paint your nipples if you are breastfeeding, or else you can re-infect each other.
Sterilize all bottles, nipples, and pacifiers (anything that goes in baby's mouth) regularly until infection is cleared up.
You can also call your pediatrician for a prescription of Nystatin - oral suspension for baby and topical ointment for you. Oral suspension is syringed into baby's cheek and rubbed in with a Q-tip, four times a day for at least three days. Topical ointment is applied to your nipples 2-3 times a day for at least three days, but has to be washed off before nursing or pumping.
Hope this helps! If it's stubborn, you may want to treat for three additional days after symptoms disappear.