This is not possible.
When installing software under Windows it installs certain files in various directories such as windows\system end of course program Files. Certain programs that run without shared files can be installed in a separate directory and you only have to make a shortcut in the other version, but those programs have become scarce since the era of Windows (under DOS this was much easier).
Besides this, some programs use different files under windows 98 and Windows 2000, since they are different (that is why some programs may cause problems under Windows 2000 (InCD from Ahead for example).
You can set your data dirs to a separate partition of your hard disk. So that all file saves will be stored on that particular partition.
So I am afraid you have to install the programs both under Windows 98 as well as under Windows 2000