Thanks for the suggestion. I think it would work--if it would work. Perhaps you can tell what I am doing wrong:
First, I created a ctrlr directory alongside the mess.exe, as this is the directory that is specified (although it did not exist) in the mess.ini for ctrlr files.
Second, I used the in-mess GUI to configure keys/joystick settings how I want them for a particular software image and verified the information is updating the apple2ee.cfg file which gets created the first time I launch mess using the apple2ee machine type.
Next, I copied this config file (actually, I made a copy, then deleted the file so MESS woudl create a new one with defaults). I used my "configured" copy and placed it into the ctrlr directory using the same-name-as-my-software.cfg.
Finally, I inserted a "-ctrlr" switch in my FE command line so it should look like:
MESS.EXE -ctrlr softwarename apple2ee s6d1 softwarename -skip_gameinfo -nowindow -nonewui
MESS launches, the machine boots, the software loads--but when I check the key configuration, it's just using the default it recreated (a new cfg file returned, as expected, as apple2ee.cfg).
So, am I doing this right? It seems like either my specified ctrlr file is getting overridden by the machine .cfg file or my syntax is wrong. The fact that the machine boots and the software loads makes me think I must be close. Any ideas?