Mike,
The new .ini location follows the Windows' one:
/home/<user>/.wine/drive_c/users/<user>/Application Data/.
Personally, I run the clean version the way the installer made the launcher, and the custom version like this:
env WINEPREFIX="/home/<user>/.wine" wine Z:\\opt\\Progs\\LTspiceIV\\scad3.exe -nowine -ini Z:\\opt\\Progs\\LTspiceIV\\scad3.INI
( -nowine because I can resize the components' dialogs, with the downfall of traces when moving symbols -- minor)
Vlad