If they are red and don't look good then that points to infection. A possible short term treatment with Cephalexin or another antibiotic from the Vet would help. Bug bites of any type if repeated set up allergic reactions. Thus start using Benedryl to control the reaction to the new bites. The Vet may recommend 1-2 mg/lb. Finally a precription salve such as Panalog will help to treat externally. If excessive licking of the salve is a problem then after applying it (Panalog is oil based), then apply a thin film of a 1:3 dilution of tea tree oil. The astringent taste is quite unpleasant and the licking will stop. On open wounds it can burn, so be careful.

The Skin So Soft product has a Citronella component that repells (or deters) some bugs. You could try that or there are now Botanical insect repellants with higher concentrations of Citronella in them. Either way you might end up with a greasy mess. More likely once the skin recovers and the allergic reaction calms down that will be sufficient for puppy dog.