At Your Destination
At last, you've arrived at your destination. Let the fun begin — right? Well, yes, but not quite. When you arrive at a hotel, motel, inn, or bed and breakfast with your dog, the first thing you want to do is let her out so she can relieve herself. Be discreet, and take her to a somewhat out-of-the-way location if possible. Other arriving guests may not appreciate watching your beloved urinate on the flowers lining the walkway to the front door.
It is absolutely necessary that you pick up after your dog when she defecates on public property. Nothing will cause an establishment to retract its “dogs allowed” policy faster than the neglect of owners who don't clean up after their dogs.
With her immediate needs taken care of and her waste properly disposed of, put your dog back in the car while you check in. Until you get the feel for the establishment, don't assume that everyone staying there will think your dog is the cutest and best-behaved they've ever met and will be thrilled to see her. In fact, assume the opposite. People checking into hotels have luggage, kids, agendas, and business meetings they need to get to, and often the last thing they want to deal with is your dog wanting to say hello. Give them the benefit of the doubt and keep things as calm as possible for everyone concerned.
At the front desk, remind the staff that when you made the reservation you asked about your dog and let them know that she is with you. They will probably have a note about it. Once you've found your room and are satisfied with it, then get your dog and bring her (and her stuff) to join you.
Settling In
Another thing hotels don't look too kindly on is damage to their rooms by unruly pets. Soiling, chewing, excessive shedding, towels that look like they've been used to bathe the dog — all of these are reasons hotels won't allow dogs. Be considerate and conscientious during your stay. Put one of the old towels or blankets you carry on the bed if your dog is going to sleep on it. Make sure he gets plenty of exercise to release some pentup energy. Feed him in the bathroom or on a noncarpeted part of the room so any spills will be easy to clean up. Consider ordering room service so you won't have to leave him in the room by himself while you get something to eat.
Going Out
The strange smells and sounds of new environments make dogs anxious. They need to explore to become more familiar with everything before settling down. Don't think you can check in, drop your dog with your luggage in the room, and take off again. For even well-mannered dogs this can be torturous.
At the same time, your dog should be well-adjusted enough that you can trust her to stay alone in the room for a few hours. Make sure she has been sufficiently exercised, that she's relieved herself, that she's had something to eat and drink, and that there is nothing in the room that could harm her while you're out. Close the door to the bathroom, put anything she might chew on in a closed drawer or closet, leave a light on, and leave the TV on for background noise (not too loud). Be sure to put the Do Not Disturb sign on your door so the staff won't come in.
The safest and most secure way of leaving your dog in your room while you go out is to put him in his crate (another great reason to crate-train your dog). His familiar crate will help him feel at ease. Knowing that he's secured in it means you won't have to worry about him getting into anything dangerous, making a mess of the room, or accidentally escaping should the staff enter your room.
When you return, tell her what a great doggy she is and take her out immediately to stretch her legs and do her thing. Be careful walking your dog after dark. Stay on lighted walkways and pay attention to landmarks so you don't get lost. Consider that you may come across local wildlife like skunks or deer — or other people's dogs or cats. If your dog can't be trusted to handle these encounters appropriately, only walk her where it seems safest.

