Yes, you pay one $25 fee to change your itinerary for BOS-CLT. If it takes you BOS-DTW-CLT or BOS-DTW-MEM-CLT or BOS-MEM-CLT it doesn't matter. You will only pay $25.

The flight options will be displayed to you when you do OLCI or check-in at a kiosk at the airport. NW doesn't have to keep you to the routing you originally had (e.g. one stop instead of two).

-RM