You can add customer specific fields by adding fields to the Billing or Shipping Customer profiles.
Via the Admin menu:
Store -> Customer profiles -> Profile Types -> Billing/Shipping Information -> Manage Fields.
URL: yoursite.com/admin/commerce/customer-profiles/types/billing/fields
If you need to customise the checkout form further, there are a number of ways, including the following:
1) Use an existing Commerce module that provides extra fields or checkout "panes".
Commerce Agree Terms - Adds a Terms and Conditions checkbox
Commerce Extra Panes - Lets you load nodes within the checkout form
2) Create a custom module and add your own checkout pane. In this pane you can add any required fields. This tutorial provides further details on how this is implemented. http://atendesigngroup.com/blog/custom-commerce-checkout-panes
3) Use the standard Drupal hook_form_alter() to modify the existing checkout form. There is an example here https://drupal.stackexchange.com/questions/107310/how-to-alter-commerce-checkout-form-in-a-custom-module