You usually want to prioritize changing the container’s build config instead of getting into them and modifying them. Much better to get into the mindset of them not being pets you have to nurture.
Separating the different services into containers is overall a good practice but having the DB in one can be a pain as it’s easier to work with stateless applications. The isolation aspect is very valuable as its easier to debug a problem. I would look into container orchestration if there isn’t already and making sure logs are centralized first.