It is easy solvable, but its one of the emulator which take a bit longer time to get work property in some Fe's. And if there is a problem, its more a Fe's fault and not the Daphne fault, which nicely can been invoked a Daphne game directly from a frontend, but just require more commandline than Else wise normal.
The major problem is really the framefiles which should been named the same as roms files to been run propenty.
If the FE doesn't support commandline or editable commandline files, it a FE issue and should ask author of that to get it running. Its not a Daphne fault.
In MultiFE, it mostly out of the box and is choiceable to run it with 640x480 or 640x400 without edit the profile as it do that nowand also I created a NMS file as well (title, year and company info). I was simply guess it these resolutions most would use with Daphne anyway.
A more problem emulator is Zinc, due it use a number based to launch the game. It not really usable without useing costume created files. In MultiFE I choiced to create a config utilty for the whole emulatoer (like ZincFe, but more cabfreindly), which can launch the games as well using rom names.