#1 Don't plan on saving the notecards forever.
Put them in an inbox immediately after writing on the notecard.
At a predetermined time, manage the inbox.
Some of my notecards get stored into folders created for current projects. These folders can be digitized at a later date for archiving and searching. Though, most notecards don't make it that far.
Some notecards represent tasks. Those get recycled as soon as they are completed.
Many notecards head straight to the recycling bin. You'd be surprised how often something seems like a good idea before you write it down.
Most of my process follows the "Getting Things Done"(GTD) framework by David Allen. I highly recommend it.