Can any one explain me what is the use of Master server while creating Zone.
And if I have two different zone on GTM with two different NS record for both zone, so I want that when ever I do DNS watch for NS for any of the zone (domain) its should resolve with both Ns.
A master zone within ZoneRunner is essentially going to be an authoritative zone for the device. Any queries directed to the GTM for a record in that zone will be answered by the GTM. You'll want a setup like this:
The parent provider zone (for example, company.com) will have NS records configured for your zone (for example, child.company.com) pointing to your two GTM appliances via hostname (ns1.child.company.com and ns2.child.company.com). You'll configure A records within your master zone (child.company.com) for ns1.child.company.com and ns2.child.company.com, corresponding to the public facing listeners on your GTMs.
So when a DNS server queries the parent zone at company.com and requests an NS record for child.company.com, the parent will hand back NS records of ns1.child.company.com and ns2.child.company.com. Then DNS servers will query your GTMs since these NS records correspond to your GTMs.
I hope this makes sense and I didn't ramble too much.