You need to have root and NAND unlock if you want to do anything like that, but it is possible.
If you have NAND unlocked, you can do it with your phone running normally, but I would use ADB in your particular situation. You can also use something like Root Explorer, but it costs money.
If you do not have NAND unlocked, but you have toast's root, you must go into recovery first.
If you know how to use ADB and you have full root (w/ NAND unlock), you should be able to use a command line in Windows to this effect.
adb shell cat /sdcard/ringtone.mp3 > /system/media/audio/ringtones/
For notification sounds:
adb shell cat /sdcard/notification.mp3 > /system/media/audio/notifications/
For the files on your SD.
Otherwise you can push from the Windows itself. In command line, navigate to the area in Windows where you have the sounds and do something like this:
adb push ringtone.mp3 /system/media/audio/ringtones/
adb push notification.mp3 /system/media/audio/notifications/
If you do not have NAND unlocked, but you have root and a custom recovery, go into the custom recovery, then apply this command.
adb shell mount /dev/block/mtblock4 /system
After that, the commands above should work normally.