Adding a template for new platform

I'm trying to figure out how to compile for a new platform with a
compiler other than the gcc compiler. My environment is such that I
have my own compiler running on a windows machine, and it's own linker.
It works to change the compiler in the Makefile.Global.in file, but it
keeps wanting to link with the gcc linker, I suspect this is because I
am trying this with MinGW. Any suggestions? I considered making a
change instead to the Makefile.am before running the autogen script but
could not find this file. Is it available? Is it a plausible solution
to trying to add my own template for compilation, etc.? Please advise.

Thanks,
Patty