While some places and accommodations do close by mid October, but there are still places to eat and sleep along the way. You have to plan for them, though.
I would book all your accommodations before even starting your trip, unless you are staying in Charlottetown or Summerside - they have a lot more motels and B&Bs. There also will be places to eat, but some will be closed for the season. However, most villages have a local store where you can get sandwiches, etc.
The 2017 Confederation Trail Guide should be helpful in planning your trip.
Also, if you do an accommodation search on Tourism's website, you can enter your dates, your price range, lodging preference, area to stay and how many are in your travelling party - this generates a list of availability, and hopefully you find something suitable. If you need a consult or luggage transfer, you can contact Independent Tourist Self-Guided Cycling Vacations or MacQueen's Island Tours.
You can also call Tourism's toll free line 1-800-463-4734 if you have questions.
Hope you have a wonderful time.