I'm new here too; it's not as scary as it seems at first.
Why do you keep all of your files on the SD card? That seems like a waste of money. I have two 8gb SD cards. I take about 200 pics on one then switch to the other. I upload them to my computer as soon as possible then back everything up to an external hard drive. Then, I take the pictures that I really like and put them in a separate file on both my computer and the EHD. I also put these photos on an 8 GB usb. So far I'm on my second usb. Each time I upload my photos to my computer (After backing it up to the EHD) I completely swipe my SD card. The digital copies are stored as year-season-date. An example would be 2010/winter/12-29. If there's a special event or something then I'll label it as 2010/winter/Christmas.
This has worked well for me so far. Perhaps one day I'll find a better way of doing it, but I have no need to change. I feel secure with the number of copies I have of an image (3). Oh, and also, with digital it's easy to take way too many pictures. Just delete the crappy ones/ones that look similar to other ones. You don't need 10 pictures of nearly the same thing.
Edit: I realize you're asking more about the physical storage of the drives. I have one sd card in my camera and one in the little plastic case that the sd card came in. I put this plastic case in an appropriately sized zippered pocket in my camera bag. For the usb drives, I have a drawer organizer in my desk drawer, and they have a "special" compartment.
Good luck, and I hope you're enjoying your new hobby! :mrgreen: