How to find which DNS server I am using (of the multiple configured dns servers)

I guess the best solution is to go to dnsleaktest and click on Standard test. I use this method personally all the time.

Windows queries DNS in this order:

1. Hosts file
2. Local DNS cache
3. Preferred DNS servers
4. Other DNS servers (Secondary, Tertiary, ...)

You can find out more about this behavior over at Microsoft (How DNS query works, Client features). Additionally, there's also a list of timeouts for DNS requests:

Value        Default Value  Attempt
-------------------------------------------------------------------------------------
1st limit    1 second       Query the preferred DNS server on a preferred connection.
2nd limit    2 seconds      Query the preferred DNS server on all connections.
3rd limit    2 seconds      Query all DNS servers on all connections (1st attempt).
4th limit    4 seconds      Query all DNS servers on all connections (2nd attempt).
5th limit    8 seconds      Query all DNS servers on all connections (3rd attempt).
6th value    (Must be 0.)

Windows may log a DNS query timeout somewhere in the Event Viewer, I'm not sure about that. Wireshark mentioned by @BBlake probably is your best bet to quickly get your answer.

The nslookup command from command prompt will tell you which one it is using (typically your primary). Sometimes typing in a fake domain (hdhsgdh.com) will fail on the first dns server and attempt to use the second.

A quick edit: don't type an address after The nslookup command, it will tell you which dns server it is using.