Separating the .cpp of the .h file is not always a good solution. Generally I separate both of them when it is used as a library (public header in include and private header with the source code).
If it is a library, this structure is ok.
lib/ (class implementations *.cpp .h)
include/ (class definitions *.h) <- Only those to be installed in your system
tests/ (main.cpp for quick tests)
doc/ (doxygen or any kind of documentation)
If it is a application
src/ (source for the application)
lib/ (source for the application library *.cpp *.hpp)
include/ (interface for the library *.h)
tests/ (main.cpp for quick tests) <- use cppunit for this part
doc/ (doxygen or any kind of documentation)
Use the flag -I$(PROJECT_BASE)/include to specify the include path for the compilation
If it is a big project, it can be good to use tool like autoconf/automake or cmake to build everything. It will ease the development.