2 OS issue

I formatted my hard drive and installed windows 2000 pro and my windows directory was Windows and then i installed win me and the directorty was window.me and after i installed it i noticed tht all my programs that i install will go on the program files and thts a problem bcuz now which ever program i install will mess up the other os as well is there any way i can prevent tht other than spliting my hard drive which is 20gb

 

yea i did my second hard drive was only 3gb

 

ok nvm tht now! i made a new partition of my 20gb
my C: drive is now 11.2gb and my E: drive is 7.35gb
i formatted my hard drive and installed windows 98 se on my E: drive and then i inserted my win 2000 pro cd and chose the clean install to have multiple os's after windows 2000 pro was finished the boot selection screen came up i choose Microsoft Windows and it says:
Invalid System Disk Replace the disk and press any key
But my windows 2000 pro is working perfectly.
Is my windows 98 se gone or can i install win 98 se again without getting rid of my boot screen selection??