I am currently trying to add some games for FS-UAE to Lutris but I am a bit stuck as to where I can add FS-UAE specific options to the game or the runner so that I can tweak the emulator to play nice with the game.
I am talking about these options here https://fs-uae.net/docs/options that are usually part of a config file related to a game. I saw that some things can already be selected in the GUI, but quite a few things like controller assignment or system tweaks are not included in the runner or game config.
Is there a guide on how to add those values to the yml files and in which format? I tried the wiki and the forum search but nothing specific came up.
bumping it after 5 days. Hope someone can help out and help me a tad here 
Lutris config only allows to set options from those selected to be in the UI. What command line option would you like to add to FS-UAE?
The usual things to nudge some games into working properly with FS-UAE 
joystick_port_0 https://fs-uae.net/docs/options/joystick-port-0
to define which controller is connected to which port, especially handy if you have more than one controller or if you need to switch the mouse over to port 0 and vice versa. Also some games require to have the mouse and joystick in the other port.
joystick_port_1
Same as above
floppy_drive_speed https://fs-uae.net/docs/options/floppy-drive-speed
This is to control how fast the virtual floppy is being read. default is turbo and has to be turned down if a game does not play well with increase read times due to timing issues hardcoded in the game
accuracy https ://fs-uae.net/docs/options/accuracy (wasn’t able to add more than two links)
To be able to run it on slower machines or to make some games run at all.
This is old and I don’t know if the OP just gave up or figured it out by themselves, but I was looking for information about this and didn’t find it clearly set out anywhere online so:
If you want to manually configure FS-UAE under Lutris, the first place to look is ~/.local/share/fs-uae/fs-uae.log
In my case that told me the default $EXE directory is ~/.local/share/lutris/runers/fs-uae which is the first place it looks for a Config.fs-uae file.
It also told me that the default $DOCUMENTS directory is ~/Documents and it looks for config files including Default.fs-uae and Host.fs-uae in ~/Documents/FS-UAE/Configurations
Another useful directory is ~/.local/share/lutris/runners/fs-uae/share/fs-uae/input where you can change controller bindings by editing the relevant .conf files.