The bootloader of Windows 98 (if configured so via msdos.sys) can display a boot menu after io.sys is loaded, but before config.sys is processed. The bootloader can even chainload another version of MS-DOS, if io.dos is present in the root directory.
Hit ALT + F, then arrow down to Save (or just hit S), then hit ALT + F, then X. The file is now updated, saved and you have exited to the C:\> prompt again. Doing all of this should remove both boot menu's from showing up.
Since Windows 9x also has MS-DOS "built in", you can just set up a boot (start up) menu that will allow you to boot to either Windows or to MS-DOS (with multiple configurations) on the same partition.