When we upload something it always goes into the "default" folder for that type (Textures for images, scripts for scripts, etc.). After that you have to drag it to the folder relevant to your inventory (assuming you have some structure there :)). Especially for bulk uploads, this can be a bit of a hassle.
When uploading, would it not be possible to allow uploading directly to a specified inventory folder you can choose on upload so that your uploads end up where you need them directly? Alternatively, adding an upload/bulk upload option to the context menu for inventory folders would make that even easier, UI-wise.