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Don't choose aisle seating. People crawl over you to get down the row or trip over your dog in the aisle because they aren't looking where they are going or can't see the dog because the lights are down. Choose putting him on the floor under your feet even if it is a squeeze over putting him in an aisle.
Center of the row is generally best because fewer people will try to squeeze past to seats on the other side of you. If there is a seat available next to an empty wheelchair slot, that's ideal because you can put your dog out of foot traffic in the wheel chair slot. Take a light colored towel or rug for him to lie on. They're hard to see in the dark and the light colored mat makes them a bit more visible. It also keeps them from getting sticky from sodas spilled on the floor.
Oh, and if any performers will be going out into the audience, give the director a heads up a dog will be there. Mr. Mephisto from Cats would have gotten quite a shock whizzing around a wall to stare at us with glowing eyes if he hadn't been warned in advance that he'd come face-to-face with a German Shepherd (who was harmless). Pa Ingalls from Little House on the Prairie came close to creaming my dog at another performance walking down the aisle in the dark singing. That's how I learned the hard way not to put them in the aisle.