Hi Leo,
I presume that Frank's using Freescale's image from one of the L3.0.35 release packages, and as far as I know, these don't point at an apt repository containing kernel sources and headers for i.MX6.
We installed our headers manually from a git tree when compiling imx-lib and friends in this post.
http://boundarydevices.com/mx6-video-acceleration/
Frank, you're going to need the sources anyway, so you can (and probably need to) use 'make headers_install' from the kernel source tree to install the headers.