Since this was more confusing than it should be I thought I'd throw this out into the wild in the hopes others in this situation will come across it in their searches.
If you have a Pogoplug (and if you don't, get one! they're awesome!) you may find yourself wanting to back up specific directories on a Windows machine to your Pogoplug. Note that on Linux you can of course connect to the Pogoplug and use whatever Linux scripts/tools you want to back stuff up (rsync being my tool of choice), but since Pogoplug does have a native Windows Pogplug Uploader tool you can use that to get this all going pretty easily on Windows.
The only tricks here are figuring out the Pogoplug terminology and then figuring out how to configure things. Nothing against Pogoplug since I know they're trying to make a buck, but by default everything you do either in the browser-based tool or in the Windows application will drive you towards using Pogoplug's cloud space as your backup. This is a perfectly valid option, and gives you the added security of having an off-site backup.
For the Windows machine in question, however, I'm already backing it up off-site using Spideroak, so all I really wanted was a way to make sure every file that gets put into the Documents directory (meaning music, photos, etc.) also makes it over to the Pogoplug. This is both as a "local" (meaning in my house) backup as well as so the music and photos can be streamed from other devices.
The first thing you need to know is "backup" in Pogoplug terminology means backing up from the Pogoplug device's drive to the Pogoplug cloud. To put it another way, you cannot (at least from what I can tell) back things up from your local machine to the Pogoplug device via the "backup" section in the browser-based tool. Also note that if backing up from the Pogoplug to their cloud is something you do want to do, you have to do that through the browser-based tool since backup options are not available in the Pogoplug Uploader that runs on Windows.
What we're looking to do here in Pogoplug terminology is sync, not backup. Makes perfect sense when you think about it. Sync options are available only in the Windows (and Mac probably)-based tools, not in the browser interface.
Let's set this up.
First, open the Pogoplug Uploader on Windows. In the top menu you'll see a "sync" button. Click that.
At the bottom of that screen there's a + button which lets you add local folders you want to sync. Click the + button and choose a local folder to sync.
You'll then see that by default the destination directory on the Pogoplug will be the root of the drive attached to your Pogoplug. If you want to sync to another location on the Pogoplug's drive, simply click the "change" link next to the destination location. This will give you the option to choose another destination on the Pogoplug drive, or you can also sync directly to the Pogoplug cloud.
Hope others find this helpful!