Food Allergy

My 1 year old cat has been diagonsed with a food allergy recently.  She's on a special diet, but manages to sneak in to where I feed my other cat and gets into his food.  It started off as a sore on her face and we were able to control it.  It has come back again, but this time has moved down her neck and she is obsessively cleaning herself bald.  I'm making an appt for her to go back to the vet and am, for the time being, removing the older cat (he is on his own special diet too) so that she has time to heal.  But there is a smell coming off her and I'm not certain what it is.  It's coming fro her neck area, and though the skin doesn't look infected, I'm not sure what else it could be.  Unless it's the smell of her saliva, since she's LITERALLY covering herself in it.  I'm not sure if the smell is associated with the allergic reaction or something else.  It's not a putrid smell, but it is rather heady and/or musty.  Any help or advice would be great.  
We do have an E-collar for her, but I'm afraid to put that on her because it will rub on the sore area.  Is there another way i can cover it?