OK- that description does help a bunch!
First off, I would tend to agree with Sean Dempsey above- I would use the dual drive
hardware RAID case from OWC too. I have one and it is a nice chunk of aluminum, would make the transport easier and I think you would be much better suited with the hardware RAID as well. You can see the enclosure in question at
http://eshop.macsales.com/item/Other World Computing/MEFW924AL2K/
Now the downside to that obviously is that it does not have eSATA ports (only FW800) so some degree of transfer speed would be lost but you might be surprised overall with the transfer speed of a hardware RAID over FW800. Now the upside to
that plan is that you do not have to figure in the cost of a SATA PCI-e card so the hookup to the home system and the university system would be consistent...
Now as far as SuperDuper incremental mode, yes I trust it completely and use it for backing up about 3Tb of drives that I use- and have been for quite some time with no problems at all. Of course as soon as I say that, your first experience will be trouble, right?
The only thing I want to add (and even though you did not ask about this! LOL) since I am a fanatic about this is I would question using an internal drive bay to backup an internal drive as you have noted that you are doing with your boot drive. The logic here is twofold if both the original and backup drives are being powered by the same power supply:
1- If there is a problem with the Mac Pro power supply that happens to spike one drive it will probably spike both, potentially rendering them both damaged beyond repair- thus leaving you with zero data. Because of that, all my internal drive backups are done to external drives. Now granted the chances of that kind of problem may be slim, but ...
and...
2- Since a backup drive only needs to be powered while actively backing up (when using programs to backup other than Time Machine), I power my backups down to reduce physical wear time on them when not in use. That is impossible when used internally unless you want to physically remove it- which the drive bays make fairly easy of course. Before I had a good uninteruptible power supply I also used to physically unplug them when not in use to isolate them for insurance since we have notoriously lousy & spiky power (lots of thunderstorms, etc) in my area.
One important addition I just noticed I missed- when you said:
"So when i'm at Drexel with teh two individual drives, I can just plug each drive into a FW800 port and voila! hopefully the array will work... will it?"
Unless you are
always on the same computer there during every session of use (and you set up the Apple Software RAID for the two specific drives before any data is loaded on them) then
no, the method you described will not function as you describe.
Since you are talking about two cases, hence no hardware RAID as is provided in the OWC case, if you needed to use a different system at the university (which would not know about your software RAID) you will be out in the cold. I am about 99.7% positive that you can't set up a new Apple Software RAID with drives that already have data striped on them. Using the OWC case on the other hand would work fine with multiple university systems- just plug in one FW 800 cable on any one and you are off to the races. Any of the systems with a FW 800 port will see the enclosure as a RAID since that is handled by the enclosure's hardware.
Hope that is not all too confusing and lends a hand!