On the section 'Manage your daemon/IoT device' you can find the option 'Upload Options'. If you click on 'Upload Options' a window will appear, you will find several tweaks for the IoT daemon there, like the option to automatically start the script after uploading it. Also there is an option to clear the board's directory, this should remove all the contents of the project work area on the board.
Regarding the internet issue, I'm not sure if this is related to the XDK. When did you notice this?
How did you determine this is being caused by the XDK?