Great post Leslie.

Myself, I am an IT guy/engineer/go to guy blah-blah. Far more importantly, I have some experience with the 7440 series of Brother MFC's.
A couple of things:
The 7440n is a ethernet capable version of the thing. Even if you own it, I don't recommend using it, as it doesn't seem to play well with routers, and having a computer play print server seems to be the best way to set everything up for dependability. That said, you install the Paperport/Brother control center suite on several computers on the network, but it will be plugged into a single computer by a USB cable. The printer and the PC-FAx are set as shared printers.
With Paperport set up on all computers, setting the paperport B/W (older version) or Paperport print-to-PDF as a default printer on all the computers can now be a handy thing.
In use: With the Brother Control Center 2.0 up and running on the print server computer, you use the different settings there to change the format that faxes and scanned items appear in Paperport. For instance, you can set up the scan button on the machine to always print to a black and white PDF (or MAX, or TIFF, or JPG, or whatever). You can then, as a standard alternative choice, make the "scan" software button in the Brother Control Center 2.0 always print to Paperport as a 24 bit color jpg. This is fine for most instances, since you can then scan in patient's horrible paper document thingies into Adobe images with little thought involved, and then use the Brother control center button to scan a color image of the patients ID and insurance cards. There is another place to work (actually many other ways to do this) the scanner. My favorite is in Paperport itself. I hit the scan button, make the choices that I want in that particular instance (type of file, resolution of file, and size of the scanned document and then hit scan right there. This way, if you want a large collection of documents scanned and stacked together, you can do so. When you want to start a new stack, you close the scan utility in PP and start it again.

The same can be done for PCFAX. Use the Brother Control Center to manage these settings. Unfortunatly, there is no documentation included with these machines that covers the PC fax function, but there is a PDF that can be found in the help links in Brother Control Center that can get you to it. It is poo, but don't be scared to experiment with it a bit. I:n the case of PC fax, you don't want to even try to go looking for a menu to control stuff on the machine itself...It doesn't exist.

Remember, that when you create a PDF with this program, the PDF is still just an image. It is difficult to clean them up or edit them. If you really need to capture text from them, look at that little notepad icon on the bottom of the screen in Paperport. That is the OCR printer...in short something that will take a scanned image and turn it into a text document. This can be very helpful to grab PMI etc... for cut and pasting (and of course editing after verifying the data). Learning to digitally sign imported documents (helpful with things like event/holter monitor reports and the like) with Adobe is nice, but be aware that Paperport, and even MS Paint can allow you to do this as well.
In closing: A well rounded suite of office software that nicely compliments AC is OpenOffice.org . This will give you far more dependable document handling and power than MS Office, and (despite what some say) even works very well with Dragon and other programs if you make some custom user settings.

Personally, I would rather have nothing but HP printers in my office. That said, there seems to be no other choice for PCFAX in a laser printer. If I REALLY had my druthers, I would not have a printer in the office at all, and only a modem with PC fax for receiving faxes from those hopelessly lost individuals that seem to think that HiPPA says that they can fax stuff but not e-mail it. That is, of course, total squat. Not only can you e-mail it, but technically you do not even have to encrypt the files that you send. Fax has a fraction of the security that e-mail has (I am really talking about when you run your own server with hmail or the like running on it, not when your office has a "Yahoo" account). What is more, you can use password protected documents in either pDF, or Open office format and send them anywhere.
Other free software that is really nice to use in electronic transmission that far and away satisfy the "reasonable measures" of security that HiPPA requires:
PeaZIP. Allows you to package files into a zip file and then password protect them with 128 bit encryption.
TrueCrypt: Software that allows you to make secure "containers" for files, virtual drives, and even hidden operating systems. This is a MUST for anyone transporting data on a laptop or or on a thumb drive. This program can not only hide a pack of files on the computer, it can hide the whole hard drive. The department of defense could not prove with any certainty that you even have any data on your computer with it protected this way ("plausible deniability"). It's nice to know that if you dropped a thumb drive out in the parking lot with your bosses' mother's medical record on it, it would be totally unreadable to outside persons. Likewise, if your network got hacked, and everything got horked off your server, the data would be just a bunch of random noise. Of course, if they can figure out exactly what 1000 digit prime numbers were factored then used to encrypt the data, they might be able to figure it out, but only if they have a few years of supercomputer time, a lot of luck, and knowledge that the files are there in the first place.