More than likely a stupid question but...

[Vazok Goregrin]

Does a Skeletal Champion Dragon have a breath weapon? If not what undead template would need to be applied for it to have one?

[xenlev]

My mind first goes to a dracolich. Never looked for one or happened across one in the books I have, but found this - http://paizo.com/threads/rzs2kccs?Dracolich-Template

Does that help?

[voideternal]

The skeleton template loses all Special Attacks, such as a breath weapon.
The skeletal champion template does not contain text that says they lose Special Attacks, so I would assume a skeletal champion dragon has a breath weapon.

You could also use the Ravener template.