Learn Croatian: Novčanik nije tamo. - The wallet is not there.

In Croatian, the word ne (not) and the word je (is) merge into a single special word: nije (is not). You will use this merged form whenever you need to negate je.

How does this sentence connect to the Gdje je...? (Where is...?) questions we're learning?

This is a perfect example of how to answer a Gdje question. If someone asks Gdje je novčanik? (Where is the wallet?), you reply by keeping the subject (novčanik) and swapping the question words for your location information—in this case, nije tamo (is not there).

Could I say Novčanik je ne tamo to mean "The wallet is not there"?

No, that sounds unnatural in Croatian. The negative part almost always attaches to the verb rather than the location. You must negate the verb "to be" by using nije (Novčanik nije tamo), rather than putting ne next to the word tamo.

Does the form of novčanik change because it is in a negative sentence?

No, it stays in the nominative (basic dictionary) form. Unlike some other Slavic languages that change the noun's ending when a sentence is negative, Croatian keeps the subject exactly the same whether you say je (is) or nije (is not).