If it won't work under the Windows 2000 DOS emulator at all, there is no hope of tweaking it to work. You may have some limited luck in manipulating the settings of a shortcut to launch the DOS app, but probably not.
It is possible, but very tricky to install Windows 98 onto a system after Windows 2000 is already present to create a dual boot. Windows 98 MUST be installed on drive C, the active boot drive of the computer. If Windows 2000 is already on that drive, you must go to a third-party partitioning management tool. System Commander from V-communications (www.v-comm.com) can be used to trick your system into supporting Win98 and Win2000 even if you installed W2000 first onto drive C.
If you don't want to go to a third party tool, you'll have to wipe the current configuration, install Win98 onto its own partition (i.e. drive C), then install Windows 2000 into another partition. You must keep the drive C partition as FAT or FAT32.