Indexing preferences generally associate each data source with a type of indexing technology and/or with an index/catalog and/or with a computing device that hosts the index/catalog for tracking backup data generated from the source data. Indexing preferences govern which index/catalog receives transaction logs for a given storage operation. Thus, indexing destinations are defined granularly and flexibly in reference to the source data. Load balancing without user intervention assures that the various index/catalogs are fairly distributed in the illustrative backup systems by autonomously initiating migration jobs. Criteria for initiating migration jobs are based on past usage and going-forward trends. An illustrative migration job re-associates data sources with a different destination media agent and/or index/catalog, including transferring some or all relevant transaction logs and/or indexing information from the old host to the new host.