Wrong board, you want the DS - Emulation board.

Besides that, are you genuinely playing Mother 2, or just EarthBound? EarthBound is kind of sketchy in SNEmulDS, your experience is basically typical: you have to spend time switching layers around if you want to play though the entire game. On the other hand, if you're actually playing Mother 2, in Japanese, you'd be better served by the GBA compilation Mother 1+2, which will get rid of all your emulation problems, largely because it's not emulated.