Preheat the oven to 350 degrees. In a 9x13" pan, add the pretzels, sugar and melted butter. Stir together to coat, and then evenly press into the bottom of the pan. Bake the crust for 10 minutes. Remove from oven and let cool completely.
While crust is baking, empty Jell-o into a bowl, and add boiling water. Stir to disolve. Set jell-o aside to cool to room temperature.
With a hand or stand mixer, cream together the cream cheese and sugar until fluffy and smooth. Gradually add in the whipping topping and mix until completely combined. Spread mixture evenly over the cooled crust, making sure filling is sealed to the sides of the pan. (This is important, as you don't want the jell-o liquid to leak to the bottom, making the crust soggy.) Refrigerate crust and cream cheese mixture for 30 minutes to set.
While crust and filling layers are chilling, slice and pit the fresh cherries and add to the cooled jell-o liquid. When the 30 minutes is up, pour the cherries & jell-o over the cream cheese layer, and chill for at least 1-2 hours or until jell-o is completely set.
Garnish with whipped cream and additional pretzels, if desired. Slice into squares and enjoy!