If the monitor is truely auto switching you'd just need to run your emulator (M2 for example) at the native resolution and your monitor should just sync. MAME will downscale 25khz images to an interlaced 15k image unless you use cabMAME by sailorsat.
Most dual res monitors I have seen though have a manual jumper on the chassis for switching and if that's the case I'd forget about it. It's too much hastle like italie says.