Did you read Validating, Rebuilding, and Filtering ROM Collections? If not, it could help you understand the basics and some specifics about building a romset. The article uses a MAME romset for example, but you can use most if not all of the tools mentioned there also for console romsets.
I use RomCenter with full no-intro romsets (i.e. with all regions in them) and Parent-Clone XML no-intro dats to build a regional mix of my liking. RomCenter can priorize the regions, e.g. use the US version of a game if available. If it's not, use the Japanese version, then the Australian, than the European and so on.