Emeka...I don't think you need to post this to the Motion Control Group...it is a LV/DAQ issue. The problem is probably going to be the number of counters available to you. Normally when you read an encoder input you need to have at least 1 counter per encoder. Then you can use event counting to determine the position of your encoder. Then you need to use a counter for each PWM output that you need. The 7041 only has 2 counters which means you could only do 1 input and 1 output at a time. You can do PWM using Analog Output channels, but that takes a little more processing (and is trickier) and you wouldn't be able to run as fast. If you went with this scenario you could use the 2 counters for 2 input encoders and 2 AO channels for the signals to your motor. There are some examples in DAQmx which show how to do this (the PWM). See the DAQmx>>Control section in the example finder.
StuartG