As I said on a m i g a w o r l d . n e t, you don't need an *installed* version at all. Simply copy the contents of "ATOMIC15:ATOMINST/" to the place where you want to install Duke3D, then install the amiga version over that. Also, make sure when editing the duke3d.cfg that you save it in DOS text format (CR+LF).
Edit:
@Moderators
I can't believe a m i g a w o r l d . n e t gets censored out like a swearword... isn't that a bit childish?