First off, that should be on ds, not 3ds part of the forum
If your card has a way to run nds files on boot, without you clickink on something, and I think you should have something with that on your current launcher's config file, then just place ysmenu nds file and folders on root of your sd card and auto run it by changing the config. Thats what I did. Just put the card inside your phone, use the file manager of your choice and download nds file and folders and place them on root if sd card
The android phones create some weird folders on the card, so if it annoys you then you should delete them on the ds itself... for example the lost.dir, android, (and I think) dcim folders