Gorrre: I'll post this one in here since I had some headaches with this problem.
I really wanted to be able to launch KeeperFX trough Heroic launcher and to log game hours in on my account, but didn't find any straight forward instructions for this for gog platform.
There is a file named goggame-<somenumbers>.info file in game directory that I am not quite sure for whom it belongs, Heroic launcher or gog. Inside of that file there are listed the launching options you can choose when launching the game, now all you have to do is, copy and paste the original Dungeon Keeper Gold entry and paste it and modify the name and path on the new entry.
Just discovered your post coming from Linux setting up Dungeon Keeper Gold with KeeperFX via Heroic and was looking for infos about the process including how the playtime can be logged. Thanks for posting this I guess! :)