How to deal with configs in non-standard locations

[Shawn Sörbom <shawn@sorbom.com>]

Hi,
I am playing with the Snes9x source code, and I can't get it to compile via 
debhelper. Snes9x has its config files in a subfolder of the sources called 
"unix". 
What is the proper way of overriding dh_auto_install and dh_auto_build to 
point debhelper to the correct location?


I have tried placing these overrides in my debian/rules file, but they don't 
seem to work:

override_dh_auto_configure:
	DESTDIR=$(shell pwd)/debian/snes9x
	cd $(shell pwd)/unix
	autoreconf -i
	configure --prefix=$(DESTDIR)

override_dh_auto_build:
	 cd $(shell pwd)/unix
	 make