I'm not sure for the zip source package, but at least for the sources installed from the online installer the headers of QtMultimedia are placed next to qbase directory, not inside it.
Also, to make your life easier you should use a prefix in your configure step and after compilation call 'nmake install' i.e.
This would build Qt in the current directory and then copy over everything needed in their right places to the prefix directory. You can then safely delete the build directory and save a lot of space, since it contains all the intermediate build artifacts that you don't need. All the includes would be placed in a single <prefix dir>\include directory for you, such as they are in the precompiled packages.