It is very hard to upload sketches wirelessly. I tired for a few days over xbee.
The problem is the Arduino needs to reset and start receiving code at a specific time. You can try and time it but I couldn't.
With the Xbee you can use a DIO to do a remote reset, but the bootloader doesn't leave enough time so sparkfun.com has a updated bootloader that allows more time to allow for wireless upload. It might work for BT. It is really unfortunate because for me it would make thinks much easier and I am sure for many others.