Cubik Studio

I have just purchased CS and am looking to use it for making minecraft models. I saw a tutorial showing that I have to replace the texture with that of an apple lets say. So instead of an apple it would show the custom model. I have a server that is going to have a bunch of custom items, but minecraft vanilla items are also important to gameplay? is there a way to assign the models to a custom id? something that doesnt already exist in minecraft? (so I can have 50+ weapons/armor and still use all the vanilla items as they are.

Unfortunately you can't have custom armor MODELS in vanilla minecraft. You need modded for that.
You can have infinitely custom weapons etc etc. (And hats)
You can use a diamond pickaxe and then with a damage value (so the durability) to map them to custom things.