The best way to think about this is the following:
1) Hyperledger Fabric v1.1 supports writing chaincode in two languages: Golang and JavaScript via Node.js
If you want to do all of the heavy lifting yourself, you can write straight chaincode.
2) Hyperledger Composer provides a higher-level model-driven language for developing smart contracts. It currently only allows deployment of these artifacts to Hyperledger Fabric. It also happens to support writing functions in JavaScript as well.
So if you want to start from a higher-level model-driven approach, Hyperledger Composer is the way to go. If you want to write all of the plumbing yourself or use very low-level chaincode features, then using chaincode itself is the way to go.
Moving forward, we are looking at a better way to move between the two and not force a decision / direction up front.