You might want to search the Knowledge Base on the NI's Support Pages for "Cable Mapping for a 68 Pin Connector to a 50 Pin Connector". This should take you to a link that will explain the mapping of a 50way to 68way cable and subsequent lines you are looking for ( reference sub link 68F50M), I guess you have SH6850 cable connected from the AT-MIO16 card to the SCB-68.
Please check out the information about the pin outs, that should help you work out which pins map to the counters, eg GPCTR0_source would be pin 37 on your SCB-68
Regards
Joe (NI)