Many journals require you to submit figures associated with a article manuscript in a way that does not allow for a separate graphics subdirectory. However, many people work with LaTeX such that they have a separate directory which is only for graphics generation and then include the resulting PDF files into their main work.
Here is a small script that takes your LaTeX file as argument, scans for included images and copies them to the directory of the LaTeX file. The LaTeX code is updated accordingly.