I’m using the Duke 3D: Atomic Edition v1.5, because it contains an additional episode, but the classical version of a game should work as well.
Most of the ports require a GRP file from original Duke 3D game for work, so you will need to install/unpack your version of Duke 3D to some directory, for example: C:\games\duke3d\
It's also a good idea to install ports to the same directory (‘C:\games\duke3d’), so they could find all required game files without any problems.
The best choice available is HRP (High Resolution Pack) which consists of hi-res textures, 3D models and eDuke32 engine (modified JFDuke3D engine).