In short, packages/modules are usually a good thing, provided the borders between them are sensible, and provided
you have time to structure your code that way. It doesn't
hurt if you start new coding projects programming entirely
in that fashion. That way, you'll develop nice templates
and tools to help you, and once you get used to it, any
moderately big application (or set of small ones) will be
just as quick to implement that way as the flat way.