My Lady is an epileptic so I know more than I'd like to about the disease.
First, primary epilepsy in a 12 week old puppy is very rare. Seizures usually don't start until a dog is 1-5 years old. In a puppy under a year, seizures are usually a symptom of an underlying disease.
These are the most likely causes of seizures in puppies:
LESS THAN 1 YEAR OF AGE
Anomaly: hydrocephalus.
Inflammatory:
Infectious - Viral: canine distemper; parasitic; bacterial; fungal
Immune mediated
Metabolic:
Hepatic - portosystemic shunt; Autoimmune thyroiditis (early stage: TgAA
positive); Hypoglycemia; Electrolyte disorders
Toxic: Single or combination vaccines; Lead; Drug related; Other exposures
Trauma: Acute; Delayed
Degenerative: Storage disorders POSSIBLE CAUSES OF SEIZURES BY AGE
Since your puppy is a Yorkie and Yorkies are thirty-six times more likely to have a liver shunt than all other breeds combined, your vet was right to suspect that first.
Here is some information about liver shunts for you:
Portosystemic Shunts FAQ Hepatic Vascular Disorders - WSAVA 2006 Congress