Robert,
I would start with the LabVIEW example that does Analog input using an External Scan Clock, which can be found by Search Examples -> I/O Interfaces -> Data Acquisition -> Analog Input -> Continuous Analog Input (assuming continuous acquisition) -> Continuous Acquisition and Graph using External Scan Clock.
In the example, it is looking for the external scan clock at the I/O connector or PFI7/StartScan on E-series boards for the scan clock. Using a counter you have two options to route the GPCTR_OUT to the scan clock. First, you can hardwire externally the OUT pin of you counter to PFI7/StartScan and leave the example as is or you can route the OUT pin of the counter to the RTSI line and modify the example to look at the RTSI line for the scan clock (this
option will only work if using counter 0 to produce the scan clock becasue you can only route counter 0 out pin to RTSI).