You can easily edit them in Kentico without using that option. In most cases, the edits you will be making will be pretty simple and easy so IMHO it's not worth the effort if your a small team of a few developers and comfortable without having Intellisense.
Really, the only time I use these features is when I'm doing upgrades.
Regarding your confusion, if you simply click the "Store all virtual objects in file system" button, it will place all virtual objects in the file system. If you make changes in the file system, you will want to sync those changes back to the database. Check out the documentation for more descriptions.