I've only set one up. Incoming faxes got dumped in a shared (via samba) directory where the secretary would move them to personal folders (subfolders in the share).
Outgoing faxes were set up to print to a fake Samba printer, email was sent to account that did the printing w/ a link to a php script that prompted for cover page info. After completing and submitting, hylafax would send when modems were available. Had 3 modems - 2 incoming dedicated, one outgoing dedicated, and incoming would roll over to outgoing if both incoming were in use. Sent/received over 50k faxes per year for 4 years... only issues were when power was lost.