They just use different ROM banking methods. MD = Magic Desk which allows a part of the RAM under the ROM to be made available. I think the Ocean format is a bit less flexible but lets you have bigger ROM sizes (up to 512K whereas MD only allows up to 128K IIRC). Either will work fine in an emulator like VICE or Denise; it only matters if running on a real C64 with e.g. an EasyFlash or some other CRT emulator.