You can have as many content controls (not controllers) as you like throughout a document. Fairly obviously, though, if you fill them in then try to replicate them via copy/paste, the pasted copy will likewise show what has already been filled in. That is an entirely separate issue from how footers are treated. If you put a content control in a footer, it will appear on all pages of the document that share that footer. If you want to have different footers, you need to:
• modify the document's page setup to incorporate the 'different first page' and/or 'different odd and even' page settings; and/or
• use Section breaks with the footer in the new Section's 'same as previous' property deactivated.
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