Correct format, with the links between the files. The links being file names and various matching id values. The reference for that (the fzp file) is the Part File Format document on the application wiki. The general recommendation is to start from an existing part, copy and make changes. Just be aware that there are errors and inconsistencies in many of the existing parts, and unless you pick the starting sample carefully, it likely does not implement all of the features you might want to use. When I was learning this, I reviewed the reference for things that looked useful, then did searches (grep) across existing part files to locate samples that used those features, using both sides to create my parts. It is also easy to get things invisibly broken. Like right now, I am looking at one of the core parts that is being dropped when a sketch breadboard view containing it is exported to an svg image. Nobody notices until the right path is attempted.
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