Bring first 2 ingredients to a simmer in a medium saucepan over medium-high heat, whisking constantly. Cook, whisking constantly, 10 minutes or until mixture is syrupy. Remove from heat, and cool completely (about 30 minutes).
Remove pits from cherries, leaving stems intact. Divide cherries among 3 (8-oz.) sterilized jars. Whisk bourbon into juice mixture, and pour into jars, filling to 1/4 inch from top; wipe jar rims. Cover with metal lids, and screw on bands. Chill 2 weeks before using. (Will keep in fridge up to 6 months.)