Please help on adding the below name servers for my domain registered by Godaddy,

NS1.DYNU.COM
NS2.DYNU.COM
NS3.DYNU.COM
NS4.DYNU.COM
NS5.DYNU.COM

There are two name servers section at Godaddy panel,

1. Settings tab "nameservers" at which I can enter the above NSX.DYNU.COM entries (X:1-5)
2. DNS Zone File "NS (nameserver)" at which the above NSX.DYNU.COM can be entered as NS records by specifying this parameters "Host", "Point To" and "TTL".

Please advice on difference between the above two sections.

Sounds like the first option should be good enough. Did you try changing it by using the 'nameservers' tab and see what happens?
You can refer to https://www.godaddy.com/help/set-custom-nameservers-for-domains-registered-with-us-12317

Yes, tried already but upon checking out the status under my TLD within Dynu panel, still showing Warning! Domain name tradeexe.com is not using Dynu name servers!