Dynamically change config files in c# Application based on environments(dev,QA,Prod) through Bamboo
In your deployment project configuration for each environment you could add a task prior to the actual deployment which would take care of setting up the right configuration file. 

It could be a script simply copying/replacing the configuration file just as you currently do manually. The script could be invoked with some pre-configured argument to identify the environment or it could detect the environment via some environment variable configured for each the deployment, see Additional deployment environment options