Michael
Best practice is to do just what you have done - make copies of microflows, pages, etc. in a module you create. That way you can update marketplace modules with a minimum of rework, if you would like to. Also, if you want to make domain model changes in a marketplace module, best practice is to create a specialization in one of your modules and use the specialization. I typically create one module in my apps to contain all customizations to marketplace modules. The only exception to this is if I plan to make a lot of customizations to a single marketplace module. In that case, I sometimes create a new module in my app that will have only the customizations for that marketplace module.
Hope that helps,
Mike