To do any kind of post-processing, use a Run Script build phase (add such a phase to your target). Use the list of environment variables Xcode provides (you can see them when the phase runs by expanding the script's results in the build results window) to locate the binary. From there you know where its Resources file is. The rest is standard Unix command-line stuff (run the command line and put the file into the target folder).
Now for advice you didn't ask for: It's trivial to re-hash the modified binary and replace yours with the new one in the resources folder. Anyone experienced enough to crack binaries would likely just disable the call to your "verify the MD5 against a file" code anyway, eliminating the need to replace the saved hash altogether. Long story short: You're wasting your time with this approach. :-)