The checkout step is a convenient wrapper for a bash script that checks out your code. You can see the actual checkout code by expanding the Checkout code section of your job page on a previous job run.
If you'd like to modify the checkout step you can copy/paste this code from the job page directly into your config.yml or into a bash script using a run step. From here you can modify the checkout process to suit your needs. Remember to remove the convenience checkout step after adding your own custom run step checkout.