Creating usable checkboxes on multiple layers

I guess you created this document with InDesign, where form fields are dependent on a layer.

As Thom said, this is not the case in a PDF document where form fields float over the layout and the layers.

Do you mean that you use the "Layers" panel to import a PDF page as a layer? 

If so then no, you can't do it this way. When Acrobat imports a PDF page as a Layer (OCG), it is only importing the flattened page content, not the active elements, such has form fields. 

However, you can attach a form field or any annotation to an OCG.  

You need to understand a bit about OCGS to understand how all this works. What Acrobat likes to call a Layer isn't really a layer at all. What they are referring too is an OCG (Optional Content Group).  This is just a marker in the PDF file There is an internal list of these OCGs, and each one has a state that is either on or off. Any block of content in the PDF can reference an OCG name.  If the state of that OCG is off, then the content is not drawn. Annotations and form fields can also referenced an OCG, so you can use on OCG is show and hide a form field. There is a varety of criteria that can set the OCG state, including a script. However, none of these features are available in the Acrobat UI.

Fortuanately, you can find a tool here that  gives you the ability to set complex OCG properties and assign an OCG to a form field.

https://www.pdfscripting.com/public/programs/downloadsearch.cfm?searchtype=simple&searchmode=cat&keywords=recent&sortby=name&cat=Acrobat%20Plug%2DIns