From PhoneServer, click on Edit -> Configuration. Select the "MWI Settings" tab, and check the "Enable MWI" box. Enter the time you want for the "Update Period". Then select "Use In-Band Dial". You need to edit the Prefix for the "Set" and "Clear" fields with the appropriate information from your PBX. You then need to select the line number from the drop down list, that you want to use for the MWI application. Usually the last port.
Set the Unread Handling to "Match Inbox (Single Folder)".
Now click on "OK", and restart PhoneServer. You should now be set up for MWI, using your In-Band Dial Settings.