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The FXS ports should be configured under the DIAL PLAN in the ATLAS, as the USER TERM entries. The ATLAS routes the calls based on the IN#ACCEPT lists on each entry. The IN#ACCEPT is the phone number that should be dialed in order to ring a phone connected to that specific FXS port.
If you have the IN#ACCEPT configured and that is the number you are dialing, then does the Cisco have that number associated with the line? This is just like a phone line and (by default) is only providing ring voltage. If the Cisco needs digits in order to route the call you can set "Direct Inward Dialing" to "Enabled" under the IFCE CONFIG for the FXS port connected to the Cisco; and define how many digits to transmit to the Cisco when it answers the inbound call.
To trouble-shoot, you can go to SYSTEM CONFIG and EVENT LOGGING, and set SWITCHBOARD to INFO. From there back out to the main menu and go to SYSTEM STATUS and you can view the events in the EVENT LOG. You should be able to see if the call was routed to the correct slot and port or was rejected in the ATLAS' logic.
Since there has been no follow-up on this question I will assume it has been answered and will mark it as answered. If you need further assistance you can post a follow-up question on this discussion.