Mailstore Archive lets you specify where your mail is stored when it comes into Mailstore. Your storage options are: Inbox Only, Archives Only, or Inbox + Archives.
Your Archives directories are separated by time, and you have the option to store messages by month or by day. Messages stored by month are in the format Archives/Year/Month, like Archives/2011/07 (for July). Messages stored by day are in the same format, with an additional folder for each day (for example, Archives/2011/07/01 for July 1st.)