I'm sorry your dog Toby is having this problem. Scabies occur from contact with other infected animals. Often the people in the home are unaffected. You can read more about scabies here:
First, you need to learn if the diagnosis of scabies is conclusive: did they find the mites under the microscope after scraping his skin or are they making a presumptive diagnosis (i.e. common because the mites are difficult to find). Usually after one treatment, scabies symptoms improve dramatically in a couple of days. Since this is not the case for Toby, then I suspect something else is going on.
As discussed above, the diagnosis could be incorrect. I would also consider that Toby may have a skin infection (i.e. yeast and/or bacteria) secondary to the scabies which has yet to be identified and treated as that could cause him to remain uncomfortable. You should ask the specialist if they checked for that type of infection using cytology.
Apoquel and Atopica should be discontinued if that has not already been done as it can be immunosuppressive and exacerbate scabies. I do not recommend putting Vaseline on his skin as it is occlusive to the pores and can delay healing as well as perpetuate bacterial or yeast infection
You can use oral antihistamines to help alleviate itch: your veterinarian can recommend a specific one based on Toby's weight. You can also give him medicated baths twice weekly to soothe his skin. This one is my favorite:
You have to lather up and let it set for 15 minutes before rinsing well to allow it time to work. Avoid contact with the eyes
You can also use this spray in between baths to help sooth his skin: http://www.amazon.com/Humilac-Spray-Rinse-8-oz/dp/B0002YFQ3U/ref=sr_1_3?s=pet-supplies&ie=UTF8&qid=1434045332&sr=1-3&keywords=humectant
Flea control is paramount since dogs with other skin problems are going to be exquisitely sensitive to even a single flea bite. Revolution isn't the best flea control but is great for scabies. I'd advise an oral monthly flea control such as Bravecto (i.e. Trifexis and Comfortis should not be used with ivermectin which is the injectable treatment for scabies).
I hope that the information I provided has been helpful. Please remember to select REPLY TO EXPERT if you have more questions or would like additional information. It is my goal to provide you with the most complete information possible prior to you leaving a feedback rating. If you received all the information you needed, then kindly submit a rating.