We are trying to get disk IO utilization QOS data for windows servers using ntperf but we can see there are multiple Counters for disk IO so which one do we need to use for complete disk IO utilization in percentage. Please suggest!
Suggest that you read the Microsoft documentation on these counters to find the one that fits your need. Whether you look at the virtual or physical disk, whether you look at individual instances or the total, whether percentage is what you actually want, etc. are all questions that your specific situation will drive.
It's also worth asking if it's worth tracking this number. "Monitoring" should help you identify issues so they can be corrected proactively. So, ask yourself what "% Disk Read Time" of 30% would cause you to do? What would 50% cause you to do? Do either of these numbers actually mean anything that's useful in driving an action?
On the other hand it might be useful to baseline usage or to plot a graph for someone to look at who just wants to see a colored line.
And also consider getting this information from CDM - That tool presents much the same IO information but tags it with a QOS name that's platform agnostic so if you have Linux or other non-windows systems you'd like to see at the same time, you can.
You could also use Admin Console, there are more options than the CDM GUI.