./configure --help | less
Look through the configure options. Many products provide a parameter to do exactly what you need.
If there is no special configure parameter, configure will try to find its needed include (and other) files. If you installed into a location configure does not expect, it will need a little help finding it. Most products create a file with a ".pc" extension and leave it in "<path>/lib/pkgconfig", where "<path>" is the --prefix= path you specified when you built libXext. Locate it. Then set up the environment variable $PKG_CONFIG_PATH with the path to that file. Example:
If the product you are building needs several of these non-standard locations, the syntax of the environment variable is the same as your $PATH variable -- separate fields with a colon ":".
Hopefully, this gets you past the "configure" step ind into the "make" step. If you have a dumb ./configure script, it may be necessary to use additional compiler directives to instruct the compiler where to search. This is done through environment variables.
Use one or more of these environment variables:
Some influential environment variables:
CC C compiler command
CFLAGS C compiler flags
LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries in a
nonstandard directory <lib dir>
CPPFLAGS C/C++ preprocessor flags, e.g. -I<include dir> if you have
headers in a nonstandard directory <include dir>
CPP C preprocessor
CXX C++ compiler command
CXXFLAGS C++ compiler flags
CXXCPP C++ preprocessor
F77 Fortran 77 compiler command
FFLAGS Fortran 77 compiler flags
From your question, LDFLAGS and CPPFLAGS are applicable.
One final environment variable might be helpful:
Again syntax is the same as $PATH. This will probably only be needed if the make process runs a utility which needs the library.
Hope this helps...