The jbl does not seem to have any output jack..it has an input jack working fine.
but you can use the headphone jack on your ipod while it is connected to the jbl ( i think it works even with the jbl off).
BUT (another one)
really does not worth to spennd all this money to wake up with some music you like.
First of all as you can see by the posts jbl on time does not work as a wake up device for your ipod (see also thread
http://discussions.apple.com/message.jspa?messageID=3147175#3147175)
Secon you can buy for a few euros(about 30 in italy) radios with an USB port and you wake up with your music on whatsoever usb key. (it looks even nice..kind of an old style radio).
To speak direct i do not suggest to buy a JBL ontime. I know it is sad to say this on this forum but it has a lot of problems.