Note the following changes in the buildfiles that you use with mkifs to create OS images:
[type=link] /usr/lib/ldqnx.so.2=/lib/libc.so.4
Change it to this for your 64-bit targets:
[type=link] /usr/lib/ldqnx-64.so.2=/lib/libc.so.4
[virtual=x86,elf]
Change it to use multiboot:
[virtual=x86_64,multiboot]
For more information, see the entry for mkifs in the QNX Neutrino Utilities Reference.