Fork repo to your account. Go to the main repo and click the Fork button.
Thanks to GitHub, making small changes is super easy. After forking the project navigate to the file you want to change and click the Edit link.
Change the file, write a commit message, and click the Commit button.
Now you need to get your change accepted.
If you are submitting features that have more than one changeset, please create a topic branch to hold the changes while they are pending merge and also to track iterations to the original submission. To create a topic branch:
$ git checkout -b new_branch_name
... make more commits if needed ...
$ git push origin new_branch_name
You can now see these changes online at a url like:
http://github.com/your_user_name/wordpress-google-cse/commits/new_branch_name
If you have single-commit patches, it is fine to keep them on master. But do keep in mind that these changesets might be cherry-picked.
Once your changeset(s) are on github, select the appropriate branch containing your changes and send a pull request. Most of the description of your changes should be in the commit messages -- so no need to write a whole lot in the pull request message. However, the pull request message is a good place to provide a rationale or use case for the change if you think one is needed. More info on pull requests.