I am a guide dog user, and have traveled extensively with my dogs. There are established procedures for getting your guide dog through security, and most TSA agents have been well trained on what to do when presented with a traveler using a service dog.

First, don't feed or water your dog the day of travel. This sounds mean; however, it's a lot nicer than making your animal suffer through a full blatter and/or fecal urgentcy. Remember, You may or may not have time to releave your dog during a lay over. If your dog gets really thursty, is panting, etc., ask the flight attendent for some ice chips.
While going through TSA, Maintain control of your dog at all times. At no time is it appropriate for TSA to take your dog. Place your dog on a sit stay When wwalking through the scanner, , and grabb the TSA agent's hand through the scanner machine. The TSA agent will helpp you through the scanner, hopefully avoiding accidentally setting off the machine - you will set off the alarm, if you bump in to eather side. Now that you are on the other side, with the leash passing through the scanner, call your dog. Your dog will set off the scanner because of the harness, but this is OK and expected. The TSA agent will then pat down your dog. Keep hold of the leash while the TSA agent is ppatting down your dog. Your dog will just think the TSA agent is giving him some friendly pets, and will love the extra attention.
When it comes to where your dog will sit/lay while your flying, dogs can curl up in to a nice little compact ball when they need too. There is enough room under the seat for your dog, but, of course, Bulkhead or first class is prefered. Tell the airline that you are traveling with a service animal, while you're making your reservation, so they can try to work this out before you arrive.

If you are in the process of getting a guide dog, wouldn't these be questions better suited to the people actually training you on how to use the dog?

I cannot speak for the security process, but the people I know who have guide dogs say that they end up lying underneath the seat, and are sometimes upgraded to business class for more legroom.