I just updated git with instructions and updated the early build links there too. Github readme has instructions for how to get drive going on 3DS. It's more or less the same as Switch with one change at the end. For now, you
must have the Export to Zip option turned on for it to upload backups. I haven't brought over the Switch code to zip folder backups to upload just yet. 3DS has some improvements over switch at the moment at the cost of RAM. I'm not sure how well old 3DS's with a lot of titles installed will handle it. New 3DS also has some minor speed benefits because I've added code to detect and use the extra core to run threads instead of using the same core as the main thread. Downloads and uploads are slow, but I suppose that's expected from 3DS. No amount of tweaking the threaded download code from Switch helped 3DS.
The layout is the same as on your SD card. It creates a JKSM folder with the same sub-folders on your drive. Every game/type is separate. I've been playing with it and moving saves from my New 3DS to my OG 3DS and vice versa for testing and fun. Kinda wish I did this sooner.
I still have a few things I need to get done before an actual release. Getting the Switch UI running on 3DS hasn't been as easy as I hoped.