A hybrid storage system is described having a mixture of different types of storage devices comprising rotational drives, flash devices, SDRAM, and SRAM. The rotational drives are used as the main storage, providing lowest cost per unit of storage memory. Flash memory is used as a higher-level cache for rotational drives. Methods for managing multiple levels of cache for this storage system is provided having a very fast Level 1 cache which consists of volatile memory (SRAM or SDRAM), and a non-volatile Level 2 cache using an array of flash devices. It describes a method of distributing the data across the rotational drives to make caching more efficient. It also describes efficient techniques for flushing data from L1 cache and L2 cache to the rotational drives, taking advantage of concurrent flash devices operations, concurrent rotational drive operations, and maximizing sequential access types in the rotational drives rather than random accesses which are relatively slower. Methods provided here may be extended for systems that have more than two cache levels.