My daughter's show pony is afraid of any kind of spray bottles.. especially bad during fly season. She is also not real fond of using a towel/rag to wipe fly spray on.. I have been able to spray her, but will not go into the details on how I accomplished that as I am sure it wasn't the proper way.

Any advice/suggestions would be greatly appreciated!! Thanks in advance!

Sorry but, 2 questions. Can you wash her,can you clip her. If you can its not her its you.
If you can't well-Its still you
Horses learn through consistant repetition, so if during her life fly spray or spray in general has been a big deal, she has been taught that it is a big deal. What you have to do is either teach her its not or teach her something that is more powerful than what she doesn't like. Start by teaching and enforceing that she stand still-No matter what. Stand her[chain over nose works faster but not neccessary] When she moves a foot[any foot] small jerk put her exactly where she was. You can also @ the same time use a word "stand" Not a word that means something else like Whoa,Easy... Now start with something that should make her move,kid,bike dog,spray bottle.. As soon as she moves repremand and put back exactly where she was and use the word, start over and over and over...While your doing it it will seem like its not working and is pointless, it will work. But remember EXACTLY. The feet have to go exactly where they were,you need to do the same thing each time exactly, Don't try to do it at a show or when your pushed for time Everyday,Everytime exactly. Don't use fly spray use plain water to start its lots cheaper. If you want a quick fix just for spray, tie her where she can't get loose and when she rears[she will] can't get her feet in anything. Fill spray bottle with water and staying out of harms way, spray her nonstop until she gives in and stands there. Give her a few minutes do it again just to be sure it wasn't a fluke. She will always be leary of spraying but will stand for it.
Another option all together is to feed a larvicide, I feed equitrol, my horses haven't seen a spray bottle in 6 yrs. I can have a coffee in the barn in summer set it down and come back-NOT A BUG!! All horses have to on it for it to work. There is a down side, they really don't like flys when they encounter them.

Most horse in general don't like the smell of fly spray. But Put a good halter on her with a 6 ft lead rope and take her and your spray bottle to the round pen and go to work. Start out with water, then you could do a water/vinegar mixture (for smell) then move to your fly spray. But I just start spraying them and let them lunge around me, when they decide to stop running around I stop spraying. It takes time but they figure out that it is not the acid rain they thought it was.
Or make sure she has a fly mask for her face and don't spray her at all.

Another tip some horse don't like the sound of the spray bottle or areosol can. You could dry putting your fly spray in a hand held weed sprayer that you pump up. It is quieter and goes on more evenly. Just make sure it is a new sprayer.

Is your fly spray too acidic? Is it irritating her skin? If not, spray her with it often and desensitize her to it.