Hi EthanHenry,
To echo what ZYOng said, the PID.vi can actually support multiple channels in the same loop. You can right click on the PID.vi to accept an array input. Your 1st number in array will be setpoint for channel 1, 2nd number in array will be setpoint 2, etc. Same for output. Internal to the PID.vi, it keeps separate shift registers to remember the data for each channel. You can also set different PID parameters for each channel.
Check out this shipping example: <LabVIEW folder>\examples\control\PID\Multi Channel PID.vi
BR
John
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