What is the ruling on selling CDs that include illicit content, and what is the ruling on selling them for more than the price agreed upon with the employer, without his knowledge?

The excess amount you took from selling the CDs must be returned to the store owner, because it is his right and not yours. Selling music CDs is not permissible in Islamic law, and their price is ill-gotten gain that must be spent on general Muslim welfare. You must stop selling them. If the store owner insists, then ask to be excused from selling them; otherwise, leave the job.