Given the numerous sub-projects inside Hyperledger that are all focused on business use cases, it would not be surprising if there was some confusion about which to use. This is understandable, but the good news is that for most cases the proper project to build on is clear.
By far the most popular and well-documented framework is Hyperledger Fabric. Fabric also has blockchain-as-a-service support from Amazon and Microsoft. In addition, Composer, Cello, and Caliper tools all work with the latest versions of Fabric. For the vast majority of projects, Hyperledger Fabric will be the project of most interest.
The second most-obvious choice is Sawtooth. For supply chain solutions, Sawtooth already has a reference implementation. In addition to this, Sawtooth has better support for writing smart contracts in multiple languages, whereas Hyperledger has support only for Go and JavaScript. In addition to this, Sawtooth core is written in Python. Python is a very popular language in data science, a field that is regularly paired with blockchain technology.
The final choices are Burrow, which would make a good match for technologies migrating from Ethereum, or needing to interface with the public Ethereum network, and Iroha, which would be a better match for projects that need to run a blockchain across mobile devices or other small machines.