Emulsion side up or down, you still run the risk of scratching when using the shuffle method. You took the time to expose each sheet of film, so why not develop one sheet at a time? Time consuming, but it's the best way. Multiple trays of developer is a great way when you do have several sheets to process. In the past I did up to 6 sheets/6 trays, and that was in my tiny darkroom in Japan.