Guru Medasana and Jordan Hambleton explain how to perform Kafka offset management when using Spark Streaming:
Enabling Spark Streaming’s checkpoint is the simplest method for storing offsets, as it is readily available within Spark’s framework. Streaming checkpoints are purposely designed to save the state of the application, in our case to HDFS, so that it can be recovered upon failure.
Checkpointing the Kafka Stream will cause the offset ranges to be stored in the checkpoint. If there is a failure, the Spark Streaming application can begin reading the messages from the checkpoint offset ranges. However, Spark Streaming checkpoints are not recoverable across applications or Spark upgrades and hence not very reliable, especially if you are using this mechanism for a critical production application. We do not recommend managing offsets via Spark checkpoints.
The authors give several options, so check it out and pick the one that works best for you.