I'm not sure I follow what you're saying there. If you import to a specific folder they don't all go to the root images folder, they go directly to the folder you are importing from. in other words if you create a folder called "thumbnails" and one called "full-size" and you right click over the "thumbnails" folder and choose import image, then in the navigation window go to your thumbnails directory and choose all the images in there, it will import them directly to the "thumbnails" directory in BSS. There is no confusion that way at all, images go exactly where you want them that way.
Yes, ideally we should be able to drag a folder from our computer into BSS and have it drop where we want it, be it the Images directory or a sub directory. I agree fully, but you do have full control over your image importing by doing what I say above and you won't have any issues with same named files (I have that a lot with WowSlider folders having the same name for thumbnails and full size images in different directories).