I just want to know if a Template has a Discovery Rule with its Item & Trigger prototypes and regular items and triggers. What is processed 1st?

I have a filesystem discovery template.

I am using the "regular" items & triggers to define specific filesystems that have custom threshold alerting. 

The Discovery Rule & item & trigger prototypes are to discover the remaining filesystems and apply our standard thresholds and alerts.

Do I need to Filter the specific filesystems out of the discovery rule? Or is the fact that I have specific items defined for them enough to prevent the discovery?

Thanks!