Hi Phil,
The SCC carrier is only conditioning your signals (i.e. if your signals are not in optimal ranges, bandwidth or need external excitation). The actual counters and all digital lines are controlled directly by the M-series board. This means you will never be able to refer to a counter in the SCC module.
If you route the signals of the M-Series board, is as if you had done so externally from the SCC. Look at this example and might give you more insight to how to implement it (This is software timing). The hardware timing would be doing correlation DIO. Here is an example that needs to be modified to adapt to your timing: http://zone.ni.com/devzone/cda/epd/p/id/4414
Hope this helps,
Yardov
Gerardo O.
RF SW Engineering R&D
National Instruments