Welcome to the Moms Panel! If you are looking to stay in the Boardwalk area, you will have to upgrade to a two-bedroom villa if the second bathroom is a priority. Both the Boardwalk VIllas and Beach Club Villas offer two-bedroom villas that have two full bathrooms.
If you are flexible in the location, there are two resorts that offer one-bedroom villas that have two bathrooms. You could choose from either Bay Lake Towers at Disney's Contemporary Resort, or Kidani Village at the Animal Kingdom Villas.
Hope this helps, good luck with your decision!