Firstly, I can confirm M3 Sakura runs nesDS & SNEmulDS (SNES) perfectly well (don't use Lameboy, so I can't comment). Sakura cannot run homebrews over 2MB, so it is essential to install a "multiple boot" firmware on your M3Real.
I personally use the "Triple Boot" firmware pack (M3Sakura, M3Real, iTouch), which runs as follows:
Normal boot - M3 Sakura loads;
Select "X" upon boot up - M3Real loads;
Select "Y" upon boot up - iTouch loads.
In response to your other question about sorting/browsing games, etc:
M3Sakura is superb and games will run from any folder (except homebrews - nesDS, etc. still need to be set up as per developer's instructions). You can apply the "hidden" feature of windows and select the folders & files you do not need to see when you turn on your DS (system folder, homebrew ini files, nesDS rom folder, default x & y boot files, etc.). This makes M3Sakura very neat & tidy.
You could think about sorting your DS games into genres, such as: Racing, RPG, Shooters, Sport, Puzzles, Educational, etc.