Target versus Format Overrides
For details on performing an override to customize the internal processes used to build your output, see this TechNote article: http://webworks.com/Technical_Assistance/Tech_Notes/Common/EX_ePub_Project_Format_Overrides.shtml
You can create your overrides in either the Formats folder or the Targets folder. The difference is the level at which the overrides will be applied. In the Targets folder, you create an override directory named for each of your project's targets. You may have three targets based on WebWorks Help 5.0. Each will have a unique name, and you can apply overrides in the Targets folder that will apply to each individual target.
In the Formats folder, you create an override directory named for each Format on which your targets are based. For example, you may have three targets based on WebWorks Help 5.0. You perform a Format override for 'WebWorks Help 5.0,' and it is applied to all targets that are based on that format.
So, your project might have targets that look like this:
If you put your override in "Targets/My Target 2/", then the changes will be applied only to the third target. If you put the override in "Targets/WebWorks Help 5.0/", then the changes will be applied only to the first target. However, if you put an override in "Formats/WebWorks Help 5.0/", then it will be applied to each of the first three targets.
When both Target and Format overrides are used, any conflicting files will use the Target-based override.