When I first started downloading Caches and uploading the Geocache Mangaer I was doing them one by one and I thought there had to be a better way. Then I found out you can click the "ammend to" button when adding new ones and I could upload a bunch at one time. This still seemed like a pain. Then I noticed the "Bookmark" option on the geocache website. Now I can bookmark a whole bunch of caches as I browse them and when I get a good list together, I can tell it to email them all to me in one .zip file and I can upload them all in 2 seconds. This is by far the easiest way I've seen.
I know this doesn't look like an answer to your question, but I found out the hard way about the "Default" folder of caches this weekend and had to retire early because I couln't see the caches in the park I was in. I figured out that I had to delete them all and reload them all in one folder for them all to be visible. Luckily I figured out the bookmarking system and it has made mass uploading and deleting folders a piece of cake.
Sorry if this post doesn't make sense, It sounded good in my head.