Really it doesn't matter. Auto-Import should do everything you need it to unless you have HH's coming in to some folder that wouldn't normally be picked up For example, when I play away from my desktop, I use DropBox to upload the HH files to my desktop, and they are automatically uploaded because I added a folder manually.
I think what you're talking more about is the Archiving Folder, where HEM backs up the actual HH text file. For the most part, all this is going to do is take up hard drive space. If you're really afraid of losing the data, just back up your database every so often, you can even make it automated with some programs and scripts, but I won't go there. As for finding a specific hand history, if you're trying to look through the actual HEM program, it has absolutely nothing to do with how your import folders are set up.
Hope that helps bud.