Program the DID on each stations calling party number, if you highlight the station on the left hand side you will see the area in the pane on the right about 3/4 of the way down "calling party number". Program the number there and you should be good to go as long as you are calls are routing out the T1.
Need a little more info on the call waiting. Make sure you have multiple call keys and that the busy condition is not checked on the forwarding path. This assumes that the 2nd call is simply going straight to voicemail.