Hmmm it's a bit difficult to say without knowing exactly what you are doing.
it might pay to do some background reading on gcc, option flags, makefiles, etc. but essentially -arch is an option for gcc, which is what compiles your source code.
You need to add -arch (and your chosen architecture) to the relevant gcc calls. Without knowing your setup this is probably in the configure file or possibly directly in the makefile (although I'm guessing the way you have things setup configure is building your makefile). Anyway, I'd suggest doing background reading on whatever your workflow is so that you understand each step of what is happening
Cheers
----------
Starting with something like this could be useful
http://www.eupcs.org/wiki/Introduction_To_Makefiles