Even though it has a prefix, all quantities calculated with SI use kilograms as the base unit of mass. So a joule is defined as being measured equivalent to kilograms x meters^2/seconds^2.
In real life, you can use any valid units of mass and velocity in [itex]E=mc^2[/itex] and get a meaningful result. Just keep track of what units you used and don't throw them away. You can measure mass in terms of pounds and velocity in terms of feet per second, and you'd say the energy is measured in terms of pounds feet^2/second^2. As it happens, this combination of units does have a name: it's called a foot-pound. (Why is it called a foot-pound? Because imperial units use "pound" for both mass and force. Sometimes the latter is abbreviated lbf. to say pounds of force. A pound of force applied through one foot is a measure of energy, the foot-pound.)
But really, in order to talk about quantities like energy in terms of nice units (like joules or ergs), you need to have some understanding of what those mean in terms of a small base of units like meters, kilograms, seconds, and so on.