Autodiscover module config with regular container input

Hi
(Using filebeat 7.4.2 in kubernetes/docker container env)

I was wondering if someone can guide me regarding the best way to do the following:
Using filebeat autodiscover with module templates for nginx and mongodb but regular container input for rest of the containers which include custom application as wells as third party such as kakfa.

How do I ensure the containers which are module processed are not reprocessed by container input ? Is autodiscover hints a better approach.?

Thanks
JE