If you REALLY-REALLY want to keep your Sense Apps in separate folders, you may, with some limitations:
- These applications won't appear in the Hub. You can only open them by dragging the QVF file from the folder onto the Sense Desktop.
- You can modify and save the Apps, and they will be saved in the corresponding folders.
- I recall there was an issue with using the same App on multiple open tabs, but I don't recall exactly what it was...