The implicit make rule for compiling a C program is
%.o:%.c
$(CC) $(CPPFLAGS) $(CFLAGS) -c -o $@ $<
where the $() syntax expands the variables. As both CPPFLAGS and CFLAGS are used in the compiler call, which you use to define include paths is a matter of personal taste. For instance if foo.c is a file in the current directory
make foo.o CPPFLAGS="-I/usr/include"
make foo.o CFLAGS="-I/usr/include"
will both call your compiler in exactly the same way, namely
gcc -I/usr/include -c -o foo.o foo.c
The difference between the two comes into play when you have multiple languages which need the same include path, for instance if you have bar.cpp then try
make bar.o CPPFLAGS="-I/usr/include"
make bar.o CFLAGS="-I/usr/include"
then the compilations will be
g++ -I/usr/include -c -o bar.o bar.cpp
g++ -c -o bar.o bar.cpp
as the C++ implicit rule also uses the CPPFLAGS variable.
This difference gives you a good guide for which to use – if you want the flag to be used for all languages put it in CPPFLAGS, if it’s for a specific language put it in CFLAGS, CXXFLAGS etc. Examples of the latter type include standard compliance or warning flags – you wouldn’t want to pass -std=c99 to your C++ compiler!
You might then end up with something like this in your makefile
CPPFLAGS=-I/usr/include
CFLAGS=-std=c99
CXXFLAGS=-Weffc++