When I play the game,the music quality is very low and doesn't sound as good like it does on EDuke32(I wanna play the dosbox version because I wanna play it as I remember it.It just doesn't sound like it should,whenever I try farting around the setup folder and change the music type,it works when I test it,but doesn't run the game when I try to play it.Help would be much appreciated.

It's not going to sound as good as Eduke32. Eduke32 uses high quality remastered sound files and Duke3D under dosbox uses the old Midi files.
You can still "play it as you remember it" with Eduke32 by going to your Duke3D directory and removing everything in your autoload folder except eduke32_mus.zip. Then when you start your game and choose your video mode, make sure your resolution is
"XXXX x XXXX 8bpp"

the major diffrence is dosbox emulates an old sb 16 midi chip while an windows port uses the midi chip on your modern sound card.

I figured out what it was.I forgot to have the setup and main programs run as Admin so it wouldn't save my setup and it wouldn't run right because of the same reason.Thanks for everyone's help.