I think the best way to add comments to a CSV file would be to add a "Comments" field or record right into the data.
Most CSV-parsing applications that I've used implement both field-mapping and record-choosing. So, to comment on the properties of a field, add a record just for field descriptions. To comment on a record, add a field at the end of it (well, all records, really) just for comments.
These are the only two reasons I can think of to comment a CSV file. But the only problem I can foresee would be programs that refuse to accept the file at all if any single record doesn't pass some validation rules. In that case, you'd have trouble writing a string-type field description record for any numeric fields.
I am by no means an expert, though, so feel free to point out any mistakes in my theory.