Howdy Julio!
Both
The Pirates League and
Bibbidi Bobbidi Boutique are amazing and will help make an already magical vacation even more memorable.
There are multiple ways to make a reservation and any of the Cast Members at these numbers can assist you. (407) WDW-STYLE or (407) 939-7895, (407) 939-2739 or Disney Dining at (407) WDW-DINE or (407) 939-3463.
With regards to the "best time" to book, I would suggest that you book your appointments as early in the day as possible so that your princess and/or pirate can enjoy their makeover as long as possible.
If you are planning to dine at Cinderella's Royal Table, you might try to coordinate the makeover with your dining reservation. We did this last year and it was great.
For your first-mate or empress, don't forget about the 4:00 PM Pirate Parade! It takes place each day (weather permitting) in Adventureland at Magic Kingdom and is fun for all!!
Please let me know if you need any further information. September is one of our favorite times of year to visit the Walt Disney World Resort and I know you will have a magical time!!