Hi Nirav,
If I understand you correctly, you want to trigger the analog inputs off of the encoder's Index pulse. I'm also assuming the Phase A output is dependent on the Index Pulse. If this is not right, let me know.
You will need to create a VI with two tasks, one task for your counter input and one for your analog inputs. Configure the counter input task to use an external clock and select the Clock Source to be the ai/SampleClockTimebase. An example of this is the Count Digital Events - Buffered - Continuous - Ext Clk VI found at Help >> Find Examples >> Hardware Input and Output >> DAQmx >> Counter Measurements >> Count Digital Events >> Count Digital Events - Buffered - Continuous - Ext Clk VI is the first example in the list. For the Analog Input channels, configure both channels in one task and trigger off of the index pulse. An example of this is the Acq&Graph Voltage-Int Clk-Dig Start VI found at Help >> Find Examples >> Hardware Input and Output >> DAQmx >> Analog Measurement Voltage >> Acq&Graph Voltage-Int Clk-Dig Start VI is seventh from the top.
The E-series cards are not designed for real simultaneous sampling - if you need true simultaneous sampling, I would recommend a S Series card. The way the E series cards sample is by a method called interval scanning where the convert clock is used to determine when each channel in the list is to be sampled. The time between the samples is the interchannel delay and can be set in software. A good reference for information about the Convert Clock and how to change it is:
How is the Convert (Channel) Clock Rate Determined in NI-DAQmx and Traditional NI-DAQ?
Micaela N
National Instruments