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Tools -> Options -> Accounts
Check "My contacts include users of a communications service"
Your sign in name should look something like "2000 at asterisk"
where 2000 is the user you set up in sip.conf
Click: Advanced
click the "Configure Settings" radio button
In the "Server Name or IP address" field, put the name or IP of your
*nix box running Asterisk.
Click the "UDP" radio button under the "Connect Using:" statement.
This should set you up...

After you set everything up, Messenger will have a message like:
"You are not connected to all services"

You can click this and it will open a window with three fields:
"Sign in name" should be the same: "2000 at asterisk"
"User Name" should be "2000" for our example and
"Password" should be the password you set for 2000 in sip.conf.

I hope this helped.
Stefan Johnson