Place the milk and vanilla bean in a medium saucepan and heat over medium-high heat until almost boiling. Remove from the heat, cover, and set aside to infuse for 15 minutes.
Preheat the oven to 325°F. Place the whole eggs, egg yolks, 3 tablespoons of sugar, and flour in a bowl and lightly whisk together.
Bring the milk back to a boil, then remove the vanilla bean, and slowly pour the hot milk over the egg mixture, whisking constantly. Strain the mixture into a pitcher, then divide among six 4-ounce ramekin dishes that have been coated with cooking spray.
Set the ramekins in a shallow roasting pan and pour enough hot water into the pan to come halfway up the sides of the ramekins. Bake until the custards are lightly set, about 30 to 35 minutes. The custards should be slightly wobbly in the center as they will continue to cook for a few minutes after being removed from the oven. Lift the custards out of the pan of hot water and place on a wire rack to cool. After cooling, refrigerate until ready to serve.
For the compote: Place 1 tablespoon sugar and 6 tablespoons water in a medium saucepan and heat over medium-high heat until the sugar has dissolved. Bring to a boil, then reduce the heat to low, and add the cherries. Cover the pan and simmer gently, stirring occasionally, until the cherries are tender, 4 to 5 minutes. Use a slotted spoon to remove the cherries and place them in a small serving bowl; set aside.
Mix the cornstarch with 1 tablespoon cold water and then stir mixture into the cherry juices in the saucepan. Bring the mixture to a boil, then reduce the heat to low and simmer, stirring, until thickened and clear, about 1 minute. Allow to cool for a few minutes, then pour the sauce over the cherries. (The compote can be served warm or at room temperature.) Spoon a little of the cherry compote over the top of each custard, and serve the rest of the compote on the side.