Madison was saying the states would be subordinate to the national government. This was all well understood at the time.
That is incorrect. The Federal system is a divisional government in which both central and State entities are equally subordinate to the "People" and are delegated different subject material over which they govern. In short, the States build little red school houses and the Feds build aircraft carriers. The States would be subordinate to the center if building little red school houses on aircraft carriers, however.
That the supremacy clause makes the central government supreme over the States in all matters is a common misconception which should have been resolved by the Ninth and Tenth Amendments which, being amendments, trump anything preceding them anyway.