Does the DDK's build environments pass preprocessor defines to code to specify x86/ia64/x64 for the code to use with #ifdef, etc.?
From what I've seen it does not.
However, when setting up your makefile, make i385, amd64 and ia64 directories and store your separate code files in those.
Then, in your sources file, use the I386_SOURCES=, AMD64_SOURCES= and IA64_SOURCES= vars, respectively, to specify the source files.
This works with .asm files, and should work with all other .c files as well.