In the ".ebextensions" folder create a config file or add to your existing config file.  In this example the config file is called "project.config" (the name doesn't actually matter)

Add the following to it:

files:
  "/etc/php.d/project.ini" :
    mode: "000644"
    owner: root
    group: root
    content: |
      upload_max_filesize = 64M
      post_max_size = 64M

Note you must uses spaces not tabs in this file