If you use both webmail (SquirrelMail) and a normal POP3 email client like Outlook Express or Mozilla to check the same email address, be aware that SquirrelMail will only be able to see email that the regular email client hasn't already downloaded and deleted from the server. Deleting downloaded email from the server is the default setting in most email clients.
If you only use webmail, don't worry about it.
In order to always see the same messages and saved email folders in SquirrelMail and your normal email client, you would simply need to set your email client to access your email via IMAP instead of POP3. Or you could see only the same new messages by setting it to leave downloaded messages on the server.