Goofy gui way to do it in xp/2000
windows key + Pause/Break
Advanced Tab
Settings in startup and recovery
That is basically the gui to modify the boot.ini file.
If you want to get rid of one, click edit from the same screen to get to the boot.ini file. Simply delete the duplicate and hope you didn't remove the wrong one.
For extra adventure, modify the file with your eyes closed and try to manipulate it with the power of your chi. Or you know...maybe not.