You need to first see if he is scratching on the outside of the mount or inside. I feel it will be outside which may be due to a bite from an insect like a mosquito or even a tick. As for brushing the teeth, you are not required to brush the teeth regularly, it is better to give them chew sticks etc, plus as a pup they will be teething and will need to chew stuff and hence the teeth will remain clean. Teeth are brushed so that there is no build up of tartar. tartar build up is more common in small breeds and older dogs. Its a good idea to have your pup used to the brushing experience but do it say once in a couple of weeks and that too very gently and for a very short period of time.
Any health related problems should be shown straight away to a good vet.