You can also create a config.site file in $PREFIX/share, usually /usr/local/share/config.site. Mine for Mozilla, or IIRC, where %CONFIG_SITE% points.
export CFLAGS=-Zomf
export CXXFLAGS=-Zomf
export ASFLAGS=-Zomf
export 'CPPFLAGS=-idirafter w:/usr/include/os2tk45'
export 'LIBS=-lcx -Zomf'
The -idirafter is to search the toolkit for includes after the usual locations such as /@unixroot/usr/include.