The simply answer is you cannot do that with a D3000. The D3000 is a gateway and when it receives a call from IP can only send the call out one of the T1/E1 ports. It cannot do IP-to-IP calls directly.
The more complicated answer is there is a way around this, but it is not simple and is usually not recommended. You can connect the 2 T1/E1 ports together (back to back) so that when a call comes from IP, it will go out T1 port 1, come back into unit on T1 port 2 and then you can send it back out to IP. This requires special configuration and may not work at all depending on what you want to do. There is also a quality issue with this. You will be compressing/decompressing each voice packet twice and this will add delay which could affect quality.