I am confused. Do you want to create a firmware binaries for Intel Atom D410 platform, or you want to run MS-DOS or Windows ME binaries on an Intel Quark MCU?
In the first case (develop firmware for Atom D410), you could probably do that with Intel System Studio tools, but it doesn't provide a development kit for bootloader/BIOS/bare metal development specifically (although the Intel System Studio Ultimate Edition provides System Debugger and Trace that can by very helpful for debugging the firmware). You might want to check UEFI/EDK2 or Coreboot projects that provide an SDK for bootloader/BIOS development.
In the second case (run MS-DOS or Windows ME binaries on Quark MCU), it is not possible, at least not without a considerable effort. Both MS-DOS and Windows ME provide an API, that is not available on Quark MCU. Also the MCU memory map and peripherals are very different from that of a standard PC. Also MS-DOS binaries normally run in x86 real mode, while Quark MCU normally operates in flat 32-bit mode (although I think it starts in real mode, and firmware switches it to the protected mode at very early boot stage).