You can achieve this in a couple of ways, depending on whether you are doing a Docker deploy with your own Dockerfile or deploying the Debezium image directory from Docker Hub.
Firstly, anything in the application.properties can be set as an environment variable. You should do this for any secrets you use in the application.properties.
You could also commit your own application.properties to Git and then copy it to /debezium/conf as part of your own Dockerfile. Something like:
FROM debezium/server:latestCOPY application.properties /debezium/conf