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Calibre saves files into its folder structure with its own naming scheme, so it doesn't matter how the original is named. Actually, once you've imported it, you won't ever know how it was named. That's for filenames, metadata contained in the files is preserved, as calibre keeps its own database. Even if you modify it in calibre, the book files are not modified, unless you explicitly tell it to do so.
As for modifying a file outside calibre, you can do it safely as long as you place it in the same folder, with the same name. If you have modified the metadata in the file, you'll have to tell calibre to re-read the metadata from the file (if you want).
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