If you have a fax machine hooked to your computer you typically configure it as a "printer" and whenever you want to send something by fax you select that "printer" and hit print - will ask for phone number or access address book to fax.
Faxing in is different depending on what software you have - most have some type of software which will do "fax to PC", the brother is the most talked about on the user board. The issue is to make the fax receive and not print, but instead to push to a folder - you need to choose a format, most want PDF, but not all software will do this. You would have to convert them then. The crucial step is to look at fax and determine if it needs action (like a refill) or just review - I would suggest that the folder they come in be reviewed by you or your staff and then you can move/name to a folder for import or just import yourself or act on and delete - eg look at a refill request, do in AC and then delete request.
You really need to find out what type of machine/software you have. Outgoing faxes are easy - if you have a machine designed to interface to your computer. If it is not made to be network capable you will hook it up to one computer and then "share" it.