If you want to use multiple JMeterEngines with a different CSV file per JMeterEngine, you will need to upload a different file for each JMeterEngines and use a parameter to differentiate each file.
Each JMeterEngine uses a distinct parameter ${__P(InstanceID)}. Please note that the "InstanceID" values start from 1 for the JMeterEngines. The value of "InstanceID" for the JMeter console is 0.

In the example above, incase you are using two JMeterEngine(s), you can upload files named file1.csv and file2.csv. In the "Filename" field you should specify: file${__P(InstanceID)}.csv.
The first JMeter engine will read file1.csv. The second will read file2.csv.
If this information is not sufficient, please contact our support.
