Hyperledger Indy is a decentralised identity system, while Hyperledger Fabric is a general purpose decentralised ledger that can be adapted for a variety of use cases. You wish to use Indy for your systems authentication purposes which itself runs on Fabric.
Consider Hyperledger Indy as an independent registry. The ledger is used for storing the DID's and claims, and can be deployed locally or you can also make use of the sovrin testnet. For testing, you can start a local pool of Indy nodes. Follow the getting started guide and check out the roles section. This will give you an idea on how to bootstrap your Indy network.
Once you are done deploying the Indy pool, the procedure from the end of Fabric is quite simple. Once your chaincode is invoked, it can make the appropriate authentication or authorisation calls to your Indy pool using the API provided by Indy-SDK. So for example when you invoke the chaincode for creating a new channel in Fabric, insert calls to the Indy pool to verify the identity of the participants.
Alternatively, Indy states the use of agents which will facilitate all the process handling for a user on the Indy pool, they have provided a reference implementation for the same. The agents just act as intermediateries, so regardless of what technology your system is deployed on, you can make calls to the agent for authentication or authorisation purposes.