Put the year on the outside
When several tax periods are involved, an ordinary folder label can prevent a difficult mistake. Give each year its own file and start with a simple index. List the return, income statements, payment evidence, notices, and submitted responses separately. A document belonging to another period should be referenced in a note rather than silently inserted as though it answered the same question.
Label the status of a document
A return copy is not the same as a filing confirmation, and an unsigned draft is not the same as the version that was sent. Add a short status label to your index. If you only have a partial copy, write down which pages are missing and where a replacement may be requested. This makes the file useful for review without pretending that every gap has already been resolved.
Create an entry point for another reader
Place a one-page note at the front explaining the issue you need to understand. Refer to documents by their index names so someone else can follow the sequence. Keep originals secure and use copies for working annotations. After a new notice or reply arrives, update the index instead of starting an unrelated pile. An organized file does not determine liability, but it makes the evidence and remaining questions easier to discuss.