GR,
There is such a thing as buffered counter acquisition. It works very similar to buffered analog acquisition; the only difference is that it can't be used as a circular buffer (continuous acquisition). To start both your acquisitions (analog and counter) at the same time, you'll have to set up a trigger.
To do this, you can set both acquisitions to start from the same trigger line. Then you either have to trigger the line from an external source, or do what most of us do and use LabVIEW to trigger a counter, DIO, or some line that can be fed in as the trigger. This will synch the two acquisitions. Then, once you get all the data, combine both data into one array (assuming they have the same scans/sec).
Mark