Hi All
I am using the standard tdm-gcc toolchain, which according to the manual: "TDM-GCC is a multilib bootstrap of GCC's x86_64-w64-mingw32 target, built to run on 32-bit or 64-bit Windows and generate binaries for 32-bit or 64-bit Windows.", I believe this is the same toolchain used to build the codeblocks nightlies.
I am using tdm-gcc to generate both 32 and 64 bit binaries of the same project, it works extremely well for this and I haven't encountered any mingw64 header issues at all
I could not find a solution to having both a 32 and 64 bit target in the same project, mainly due to the resource compiler. Tim's suggestion was perfect because I only have 1 resource file per project anyway
Hope that clears up the confusion