If you edit SRCPATH/debian/rules you can change the configure script that 
Debian uses to generate the package - add configure parameters, or even CFLAGS 
if you roll like that.

I find doing it this way is cleaner than building completely from source, 
because then everything still follows Debian conventions, and it can be managed 
with apt-get. I've used it to enable extra modules for nginx or PHP, for 
example.

$ cat nginx-0.7.67/debian/rules

... snip ...

        ./configure --conf-path=/etc/nginx/nginx.conf \
            --error-log-path=/var/log/nginx/error.log \
            --http-client-body-temp-path=/var/lib/nginx/body \
            --http-fastcgi-temp-path=/var/lib/nginx/fastcgi \
            --http-log-path=/var/log/nginx/access.log \
            --http-proxy-temp-path=/var/lib/nginx/proxy \
            --lock-path=/var/lock/nginx.lock \
            --pid-path=/var/run/nginx.pid \
            --with-debug \
            --with-http_dav_module \
            --with-http_flv_module \
            --with-http_geoip_module \
            --with-http_gzip_static_module \
            --with-http_realip_module \
            --with-http_stub_status_module \
            --with-http_ssl_module \
            --with-http_sub_module \
            --with-ipv6 \
            --with-mail \
            --with-mail_ssl_module \
            --add-module=$(CURDIR)/modules/nginx-upstream-fair \
            $(CONFIGURE_OPTS)

... snip ...



> Does that allow you to set custom configure flags?

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