How can I check this in the deployment.xml in Websphere. So when I deploy my application this is already checked.
The name of the XML attribute is "backgroundApplication" (it's not in there by default, as it defaults to "false"); however, deployment.xml is generated by WebSphere at deployment time, so you can't specify this setting prior to deployment.
If you script your application install through wsadmin, you could update your script to add a call to update the setting after the call to install the app. That will get the setting modified right away as part of your deployment process.