When you configure the FXS ports in the DIAL PLAN there is an IN#ACCEPT on each USER TERM entry. This is the phone number that should be dialed to ring the phone connected to that specific port. So if your IN#ACCEPT on an FXS port is 555-1111 then when you dial 555-1111 from another phone it will ring the phone connected to the specified FXS port.
If you used a 10-digit number in the IN#ACCEPT list, then you will have to make an adjustment in the DIAL PLAN under the GLOBAL PARAM in the NUMBER COMPLETE TEMPLATES. The ATLAS is set up for 7-digit local dialing (by default) so the first pattern is NXX-XXXX. If you are doing 10-digit dialing you should change this pattern to be NXX-NXX-XXXX (for a 10-digit pattern).
Hope this helps,