Thank you for your question regarding your 3 month old puppy. While there are a number of things that could be going on here that I will mention soon, this is most likely is that your girl has skin parasites or fungi, or possibly even an allergy with a secondary bacterial and/or yeast infection.
Firstly - you need to make sure you are using a flea product appropriate for her weight. Even though you cannot see any fleas on her doesn't mean there are one or two lurking and oftentimes this is all it takes for a dog with flea allergy dermatitis.So even though you applied Frontline yesterday there still may have been one or two fleas on her yesterday that bit her while they were dying. In your girls's case it does sounds like she may have an underlying allergy of some sort with secondary infection, however this could also be caused by parasites or fungi (ringworm or yeast).
Bascially dogs are allergic to four main things - food, fleas, grasses/plants (contact allergy) or environmental allergens (canine atopy - the dog version of ezcema). I always like to ensure I have talked through each of these with my clients here in New Zealand. Flea allergies are avoided by strict flea control - every 3 - 4 weeks with Advantage or Advantage Multi or every 5 - 6 weeks with Frontline. Frontline plus is perfect and this should be working already. You must also ensure all dogs in the household are treated at the same time. For a food allergy, you need to undertake a food trial with a 'novel protein' diet such as Hill's Z/D ultra allergen free and needs to be fed SOLELY for 3 weeks. After this time if you are seeing a change in your dog's allergy you can slowly introduce different foods week by week with the guidance of your Veterinarian. Contact allergies are best treated by avoidance of the plants that are to blame, but identifying the exact cause of a contact allergy can be very hard. A referral to a canine skin specialist may be the way to go in your dog's case for either a skin patch test or a blood allergen test.
It is also possible your dog may have skin mites or lice as they commonly cause intense itching and irritation. These could be either Demodex (less itchy) or Sarcoptes mites (VERY itchy) and you should ensure a full Veterinary check up so that he or she can carry out a physical examination and possibly a skin scrape to check for mites and lice, as well as signs of fleas. The next step would be to double check for fungal disease (such as ringworm) and there are several tests for this including a UV light and a fungal culture. It could also be that your dog has a bad yeast problem - and a good medicated shampoo such as Malaseb may well do the trick! Again a full Vet check will be able to confirm or deny this. If after these tests there is no diagnosis, the next step would be to carry out a food trial as above.
I really would encourage you to get your girl checked out at your Vet clinic as I am a little worried this could be mites or fleas. For the best thing for her in the mean time, as above, is a medicated shampoo that will deal with both yeast and bacteria - Malaseb (or a similar product containing both Chlorhexidine and Miconazole) is the most ideally suited for this. This requires you to make a lather and leave this lather on for 10 minutes before washing off! For many clients this is easier said that done, but it is SO important.
Please keep in touch and let me know how you get on with your itchy girl!