Got treated for scabies, put permethrin from the neck down last night, but woke up with itchy bites on my side. I think its bites or is from treatment?

Bites. Keep using the treatment as stated by your doctor, also you should use hot, soapy water to wash all clothing, towels and bedding you used. Dry with high heat. Dry-clean items you can't wash at home. Consider placing items you can't wash in a sealed plastic bag and leaving it in your garage, for a couple of weeks, this will starve the mites. Treatment will take awhile.