You have used 'difference' correctly in your opening sentence:
What's the difference between (different) and (difference)?
How are (different) and (difference) different?
What is the difference between a bull and a cow?
How are a cow and a bull different?
These are all correct but some use difference (difference) as a noun and some use difference (different) as an adjective. Think of it more in terms of where you would put it in a sentence. Sorry I hope this isn't confusing!