First, thanks for DoomRunner. Its the best I've found on Linux.
That said, from the AUR repository, when you choose Save dir "Use preset name" - I can't get it to work. It only saves in the default save folder. (this is a killer feature BTW)
As a workaround I add this to "Additional arguments [preset] which does work: -savedir "/home/MINE/.local/share/games/uzdoom/maps/Amalgoom/"