Two possible answers for you, based on traditional NI-DAQ. Either should work, though I'd recommend #2 unless there's a specific reason you need to do #1.
1. Add a call to 'Counter Set Attribute.vi' to the configuration chain. The attribute and the attribute value type should be 'up down' and 'hardware' to specify hardware control of count direction. For this to work, the call to 'Counter Group Config' should specify 'event counting', not 'position measurement.' Note that this prevents you from using the encoder's z-index pulse (if it has one) to hardware reset the count value. 2. Bypass the LS7084 and feed the quadrature A&B signals directly to your counter (assuming they are already TTL compatible). Your 6601 is designed to interface directly to quadrature signals. They just need to be wired to the counter's default Source and Up/Down pins. With this method, your call to 'Counter Group Config' should specify 'position measurement'. There's a handy config vi under the examples directory (look for something like "examples\daq\counter\ni_tio.llb") with a name like 'Counter Encoder (NI-TIO).vi' that'll help you configure for direct encoder position measurement. This method can also allow you to hardware reset your count value on a z-index pulse (wired to the counter's default Gate input).
