Would you suggest having only a few rooms as “dog friendly”?
It works well to have dog-friendly and non-dog rooms. For us, 6 of our 9 rooms are dog-friendly, and we reserve the 3 in our Main House as dog-free. This gives you the flexibility to have a room for guests who say they don't like dogs or are allergic. For us, it gives us the added benefit of saying to guests "we don't allow dogs in the Main House, which precludes them from trying to bring their dog to breakfast. You do not want dogs in your dining room. We stayed at a dog-friendly B&B that did that, and it's nothing but trouble.
Do you require crates?
We don't require them, but tell guests "You're dog is welcome to have free run of the room, even while you're gone, as long as they're not destructive or disruptive." If they are, then we even have a couple of crates we can loan guests.
Do you provide dog walking/TLC services?
Yes. Our staff will walk dogs for a tip. We have a couple of packages where we throw it in. The staff loves it (it's a break from cleaning rooms) and the guests appreciate it. We ask guests at breakfast what time(s) they want their dog walked. Then we give them a "report card" in their room telling them what their dog did on their walk (see below).
Do you charge a pet fee?
No.
Is it Refundable?
You're asking about a deposit. We don't charge a deposit, but let guests know they'll be charged for any damage. It rarely happens (Most common is dog nails scratching the windowsills when they're looking out the windows).
Finally, as a pet owner, how do you handle having your own dog at the Inn? Do you put info about him/her on your website as a “mascot”?
Maple, our tiny Shih Tzu, is billed as our "Morale Officer." When our beagles were alive, they were on the website as our "Director of Security" (one beagle howled once every time a car pulled up) and CKO (Chief Kissing Officer).
I’m most concerned right now that we have bookings this fall that would not have been apprised of the incoming dogs.
Just as we don't let others' dogs in the Main House, our Shih Tzu remains in the owners area or our office when guests are on property. She gets to come out in the living room on zero days. Dogs aren't like cats - there are a lot fewer potential guests who are allergic.
You could make your 2BRs dog friendly and leave the main house dog free. Most people traveling with dogs either have kids or want more space. We don't have a fence on the property or a dog run, and we require guests to keep their dogs on leash (you never know how even the nicest dog will interact with another dog).
Walking your dog is a good thing, better than a run or dog-door. We have a 4pm walk every day and it helps us clear our heads and reconnect in the middle of check-in crazy.
Good luck!