So I really need help with converting DDS file to NIF. I have created a custom texture which is a DDS file but now I need it as a NIF file. Do I have to convert it or I have to use other type of tools. On my case I have retextured a weapon and I want to add the textures on a custom weapon and make so it won't overwrite nothing in Vanilla Skyrim. Please Help. How can I create a NIF file from a DDS ?

A .dds file is the actual texture file, the .nif file is the object file. To do what you need you must first create a texture set containing the .dds file. http://www.creationkit.com/Retexture_Tutorial This link may help.

Okay but before I start this tutorial I need to know : this will add a new item to the game that is retextured and wont retexture any vanilla objects except the new one right ?

As long as you change the formID before clicking OK on any of the dialoge boxes of items you wish to clone and change you should be alright.