Commerce pay by check adds a pay by check payment type to the Drupal Commerce module. This module is based off the commerce deferred payment module. My particular requirements needed a specific check payment type.
To activate the payment type, visit ../admin/commerce/config/payment-methods and select, pay by check.
This modules also allows you to add pay by check information, such as the address users should send the payment.
Using rules, you can update the order state for items purchased with, pay by check. To do this, simply select the "Completing the checkout process" event, payment method "Pay by check" for the condition, and "Update order status" for the action.
TODO: Improve the manual option for allowing users to add partial payment, and have it subtract the partial payment form the total balance due.
If you have any other suggestions or additions for this module, let me know and I will work on adding them in.