The architecture of Windows 9x series OS kernel is monolithic. The basic code is considered similar in function to MS-DOS - as a 16/32 bit hybrid, it requires MS-DOS support to operate.
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The system may also use CONFIG.SYS (which contains settings and commands executed before loading the command interpreter) and AUTOEXEC.BAT (which is a batch file automatically executed after loading COMMAND.COM), but these two files aren't critical to the boot process, as Windows 9x IO.SYS contains a default setting for both, in case they're absent in the system.
The boot sequence of Windows 9x relies heavily on MS-DOS. The order of the boot sequence is:
1. IO.SYS loads, using boot parameters from MSDOS.SYS,
2. CONFIG.SYS commands get parsed by IO.SYS,
3. COMMAND.COM loads, allowing processing of AUTOEXEC.BAT (if it's present in the system),
4. WIN.COM loads the GUI (if the GUI is not disabled manually by boot menu or MSDOS.SYS setting).
The Windows 9x kernel is a MS-DOS kernel with additional support for security in memory and virtual memory. The kernel has very basic support for device interfacing. Everything that is not under the DOS 16-bit kernel is run in User space.