If I am understanding what you are saying (standard USB cable), the cable will connect to the USB port on the PS3 and the other end should fit the external HDD USB port.
In Comgenie, you can scroll down to "dev_usb006" (don't know if the "6" will be the same on yours, but it will be "dev_usb00*") and click on that to get into your USB HDD.
To use a connection from the PS3 to your PC, you have to have an ethernet cable. Best solution for this is by going through a router (if you have one). If you do not have a router, I think you will need a different type of cable (don't remember what it's called at the moment) to allow a direct connection between the two devices.
Doing it this way, you will also need BlackBox FTP or Multiman's FTP (not sure if Gaia or Rogero have FTP in them).
With what you are describing, the easiest way (without buying more cables) is going to be transferring files into the external HDD via PC and then connecting it to the PS3 and either transferring them into the internal or having the backup manager or emulator point towards the folder your files are in.
If you can use the external for primarily the PS3 stuff, I would recommend leaving the files on the external and pointing the BM to it (unless you swapped that 40 gig HDD in the new PS3 for something more reasonable ).
Sooooooo.............did you get CFW going???
I would much rather go to my grave not needing my gun, than go there wishing I had it.