I'm not exactly sure what you're asking but:
I know automapper "works best" when entitiy properties match DTO properties. But what if they don't? Can you configure it in a custom way?
If you're asking what I think you're asking you should look into .ForMember and overriding the Convert function. There are examples of both on the wiki:
.ForMember: https://github.com/AutoMapper/AutoMapper/wiki/Projection
Convert: https://github.com/AutoMapper/AutoMapper/wiki/Custom-type-converters
Automapper does work "best" when dtos and entities match up because it's super easy to set up a map between the two is their property names and types match. When they don't match you need to manually select properties with .ForMember or manually do the whole conversion by overriding the Convert function.
I hope this is a little helpful. Pop a comment below if it wasn't or you need more info.