I would highly discourage using the "copy the system files here to boot this version" method of dual-booting. You can run into lots of problems that way. For instance, say you've installed a lot of programs using Win98, and then the computer crashes (which could be very likely). Then, when you restart, you're back to before and you'd have to reinstall any software to get the registry keys back in the registry.
I'm sure you can do some fancy coding (sigh.. if only .bat files could be as cool as bash scripts) to say, "if last_operating_system == win98 and current_option == win98 then don't copy files" but that's still rather inefficient. The best way to load multiple OS's is to use multiple partitions. And Microsoft doesn't seem to want to make things easier.