Using the Classic Phonetools Software that comes with MT5600ZDX, is it possible to create a seperate mailbox for different employees in the company for received faxes?

No, the BVRP Classic PhoneTools software cannot setup up mailboxes for separate received faxes. It only receives faxes into the one Inbox.

Multi-Tech does make a FaxFinder V.34 Fax Server Appliance:

The FaxFinder is a complete, easy-to-use network fax server. Using Direct Inward Dialing (DID), it allows you to receive faxes wherever you are as e-mails and send faxes from any application that can print. The FaxFinder provides distributed faxing capabilities, over a WAN, from a corporate office to small remote offices as well as to field sales people. In addition, it provides secure, convenient faxing for LAN users offering a high degree of privacy for both the sender and recipient. Please visit our Web site for more information on this product:

http://www.multitech.com/en_US/PRODUCTS/Families/FaxFinder/