It doesn't mean it's not working. When you have a yeast infection, the discharge is your body's own attempt to purge itself... it takes a while for it to catch up with the new, fungus-free state of things. If it doesn't settle out on its own in a few days, call up your doc again to make sure you haven't just driven the fungus underground, but right now I wouldn't be concerned.
Using an OTC remedy like Monistat on top of the Diflucan isn't likely to help: presumably you were using it on this infection before, and it didn't help, so doing it again won't do you much good. However if you are still tender you can use the soothing cream and it won't hurt the effectiveness of the prescription.