First I've never programmed a 996T using the rear port. My gut feeling, however, is a serial port is a serial port. So if I was in your shoes, I'd be tempted to try it. My instincts are saying that the front port is typically used for programming purposes because it is easier to access than the rear, particularly when vehicle mounted.
Unfortunately connecting a serial cable to your computer isn't as easy as it used to be. Few computers these days have the RS-232/DB9 connector. Most likely a USB to RS-232 DB9 adapter is needed. And making it worse, if you use Windows 8, the chipset in this adapter is critical.
Here is the cabling set-up I use to connect my scanner to the rear serial ports on my Uniden scanners (780, 996XT and 536):
1. Plugable USB to RS-232 DB9 Serial Adapter (which has the Prolific PL2303HX D chipset because I have Windows 8).
Amazon.com: Plugable USB to RS-232 DB9 Serial Adapter (Prolific PL2303HX Rev D Chipset): Computers & Accessories
2. Null Modem Adapter (you have to have this)
3. Gender Adapter (may or may not need this depending upon the ends of the Serial Cable)
4. Serial Cable
If time is critical you could check your local Radio Shack store. They may have most of these things. (Just be sure if you are using Windows 8, the USB to Serial adapter has the HXD chipset).
Also, when you use a USB to Serial Adapter, there are drivers that you must install prior to its use.
I'm not that great of a computer hardware "guru", but I was able to get this to work with little effort.