I'm sorry that you are having these worries but as others have said, this is very, very unlikely to be SM. Has a vet checked out the possible sources of the scratching and found nothing that explains it, or are you guessing this is the case as you can't find anything yourself? Most of the things that make a puppy scratch are not easily spotted by owners -- especially ear infections, ear mites, rabbit mites, or allergies -- so you have a huge range of things that are more likely explanations.
Three months is about the earliest age at which SM has ever been diagnosed, so it would be extremely rare for a pup that age to be scratching due to syringomyelia (especially as for dogs that will develop it, this is a progressive disease, and dogs that do scratch may not start til they are adults).
There's lots of information that explains the condition in more detail here:
www.smcavalier.com
In particular have a look at the symptoms sheet and the 'Is this SM?' section as it lists all the things avet would want to check for first.
You are right to make a vet appointment, as you do need to figure out what is making your pup uncomfortable. It is probably going to be ear mites, rabbit mites or fleas though -- or maybe a bit of dermatitis, as puppies, like human babies, often can have a bit of itchy dry skin that clears as they get a bit older. Many puppies come from their breeder with ear or rabbit mites -- this is perhaps surprisingly common (my pup had rabbit mites).
