1- Install the game (GoG version is recommended to avoid problems) on your windows PC
2- Open Batocera folder \\batocera\share\roms\windows\ in explorer
3- Download this archive, copy it into the batocera folder, it’s just a premade wine prefix i’ve done
4- Extract it, using SSH (google it if you don’t know) using the command : 7zx x Template.7z
DO NOT try to extract it with windows 7-zip or winrar, it will fail
5- Rename the Extracted folder Template to DukeNukem.wine
6- Copy installed game folder into DukeNukem.wine\drive_c\GOG Games\
7- Edit, using Notepad++ (windows) or vim (through SSH) the file DukeNukem.wine\autorun.cmd and modify DIR and CMD lines to reflect your game folder and executable.
8- Update game list under batocera interface and play. If it do not work out of the box, edit game settings to force lutris (proton is default) and try other settings like MediaFoundation.