Well what your not realizing is, each time you install a OS, it rewrites to the MBR. If you install Win98, then Linux, it will usually detect it and go ahead and configure it. If you install NT, then 98, the loader for NT surely detects 98, but then if you install Linux on top of that, it doesn't detect Nt but will 98. so on....and so on...its like a large continuous loop. What you need to do is figure out which Loader you want to use. Maybe the NT Loader or LILO.
From there you should be able to read up on the HowTo's at http://www.linuxdoc.org
to get it all configured from there.