You need to create one IMAP account for each folder you like to check:"name"
Use aright mouse click on the SMTP account to add an IMAP account to an existing SMTP account.See also: http://www.jam-software.de/knowledgebase/5721
Just substitute the "INBOX" text in the IMAP settings of "Mailbox" by the name of the desired folder. You can also use "INBOX/subfolder" or "INBOX\subfolder" (depending on your provider) for retrieving messages from subfolders.
In the manual of SmartPOP2Exchange you can this about your question: Q: I want to leave all messages on my POP3account in order to use as a backup. Is it possible?
A: No this isn 't possible. We do not recommendthis setup, because a POP3 is usually not designed to hold large amounts ofmails and can get extremely slow. However you can use the rules engine ofSmartPOP2Exchange V6 to send a copy of every incoming message to any emailaddress you want. So maybe you can create a "backup" Exchange accountand store your messages there. For leaving mails on server the IMAP protocolshould be used. IMAP is also supported by SmartPOP2Exchange.
As the error message already explains, "Connection timed out" means the connected party (POP3 server) did not properly respond within the desired period of time.
Try increasing the value of the timeout setting in SmartPOP2Exchange. Use either the global settings or the timeout settings under "Expert settings"of that POP3 account.
Values between 120 and 300 are common for timeouts. Depending on our internet connection type/speed and if the server is busy you even set that value up to 600.