I am not entirely sure what green and black wires we are talking about... or if you're talking about attaching them on the transformer side or on the breaker side.
I found this pretty simple diagram:
http://diyhousehelp.com/how-to/plumbing-electrical-hvac/doorbell-wiring-diagrams/In that diagram the transformer has 3 wires (which is normal): black, white and (probably) green.
When you are running to the breaker panel, you will probably run regular old romex between them. (I'm assuming this is on its own circuit here.) Black on the transformer ties to black wire in romex, white on transformer to white romex, green on transformer to bare romex wire.
On the breaker end: Black goes to the new circuit breaker. White goes to the neutral bus bar. Bare goes to the ground bus bar. (Sometimes neutral and ground will have separate bars. Sometimes not.)
As usual disclaimer: I'm not an electrician. If someone replies with "I'm an electrician, don't listen to that idiot" -- listen to him/her, not me.
