I am not talking about the new Lollipop which encrypts everything by default. The older versions, such as Androd 4.2.1/4.2.2 etc. Suppose you went to settings -> security -> encryption, and chose full disk encryption. All files on disk are now encrypted. Now, if you create a new file on the disk 5 minutes later, would that be automatically encrypted right away, or would you need to encrypt it again using full disk encryption?
First, both encryptions you name are the same – only that Lollipop enforces this automatically on some devices.
Second: it's not the files being encrypted, but the entire partitions – thus everything saved to it ends up in (using simple terms) an "encrypted container". Everything transparent, so you won't notice. No need to re-encrypt.