If I understood you correctly, you are reading the two current
positions (1)-up-down  and (2) left-right,  and you have two set
points (one for the up-down and the other for the left-right position,
read by the master.  And the objective is to make the readout for the
positions as close as possible and ideally equal to the set points.
Assuming the up-down and left right positions are independent, you can
use two PID Loops to address this problem.  One for the up-down, and
the other to control the left right.
Normally, a PID loop takes two inputs:  The SetPoint, and the
corresponding readout of the system.  It calculates an output signal
(to the data acquistion system ) that moves the system in a way so
that
(The Set point =96 Readout ) becomes ideally zero  (no error).
The other parameters are the tuning parameters. They control the speed
and overshoot of the response, and they have to be properly selected.
A system that is poorly tuned may oscillate and can cause damage
(depending on the setup)
There is an example that ships with LabView and it has a basic PID
controller that you may want to look at first.
A good PID loop should have a mean of setting it in manual mode to
make it take any preset voltage (this is what you probably mean by
calibration).   The basic loop example that ships with LabView does
not have that.  You have to modify it (assuming you have the basic
understanding of the Pid Algorithm), or purchase a PID kit from some
vendors.  NI have a PID kit that also can autotune the parameters.  Or
you can get someone from your neighboring school to help you with the
algorithm

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