Auto Apply credits at checkout I am using commerce_userpoints which allows the use of credit to discount the amount at checkout of a product. 

Right now the user needs to do this manually however I would like to automate this.

Any clue on how can I get this done ?
Use rules. When the order is completed, use the actions contained in the  userpoints_rules submodule to manage your userpoints. You might choose the "When an order has been paid in full" or you could just watch for orders moving in status to "Completed."