According to the documentation for v.7 and v.8, there are several ways to accomplish what you want, and you almost have the correct rule:
Export["test.fits", {"Data" -> data, "Metadata" -> header}, "Rules"]
Other ways are
Export["test.fits", header, "Metadata"]
Export["test.fits", {data, header}, {{"Data", "Metadata"}}]
note the double brackets around the element labels in the second method.
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