Boot.ini options for Win2000

After installing Win98 on a secundary partition (primary) I had to set manually the active partition to the first partition with Windows 2000. Now I want to boot both system, without using FDisk every time to set the active bit to the right partition.
So I want to add the Win98 partition in Boot.ini.
Tried to do it, but it fails to load Win 98.
Is there a solution for it?