Thanks everyone for your responses. Very reassuring. It is helpful to hear from others who are going through what we are. Thankfully, Alex appears perfectly healthy is every other way, and the allergist we're working with is wonderful (we're in Montgomery County, MD, just outside DC, and go to Dr. Jeffers -
AADC - Animal Allergy & Dermatology Clinic | Skin Testing). The staff there have been really helpful.
For the next couple of weeks, we're doing the prednisone, slowly tapering down. We did three days @ 5.0mg, and are currently on 5.0 mg every other day. Then, we'll go down to 2.5mg every other day, and then 2.5 mg every third day. Basically, they want to do a slow taper, and then start on the Atopica. I know in humans, cyclosporin (which is what Atopica contains) is preferable to prednisone, as cyclosporin has fewer side effects. I am assuming it's the same in dogs.
Like someone mentions above, the hope is that this is just temporary. The allergy shots should be working by March, at which time we will slowly d/c the Atopica. I am hoping, hoping, hoping the allergy shots work because this little guy has had a rough life and deserves to at least be itch-free!
We are also doing a weekly anti-fungal bath, as Alex's last skin slide showed a skin yeast infection. Has anyone else had trouble with this? He definitely was starting to develop a yeasty smell, which has since gone away with the anti-fungal baths (he also did a course of antibiotics and a course of oral anti-fungal medication).
One more thing - we just got back from the beach and Alex was so much more comfortable there. I don't know if it was the salt water or what, but he was really, really happy. Maybe we should just move to the beach