I was able to install 2 layouts....1 for mame and 1 for atari 2600.
When I switch emulator, the layout change

This is the structure that I have used:
C:\Games\Mala (this is were I put all the mala file + all the .mll file for the mame and atari 2600.....if you download a layout for mame and that the name of the .mll is something like this gala640.mll.....you have to rename that file the same way as your folder name.....mame.mll)
C:\Games\Mala\Mame (this is were I put the graphic file for the mame emulator like bg.jpg...etc)
C:\Games\Mala\Atari 2600 (this is were I put the graphic file for the atari 2600 emulator like atari2600.jpg...etc)
C:\Games\Emulator\Mame (this is were I put all the mame program file and emulator)
C:\Games\Emulator\Mame\Roms (this is were I put the mame roms)
C:\Games\Emulator\Mame\Snaps (thsi is were I put the mame snaps)
C:\Games\Emulator\Atari 2600 (this is were I put the atari 2600 files and emulator stella.exe)
C:\Games\Emulator\Atari 2600\Roms (this is were I put the atari 2600 roms)
C:\Games\Backup (all my backup files)
Sometime, you have to exit and reenter mala program in order to active the new layout that you have just put....
Good luck