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2. To run the emulators, do I need to have an emulator in the same folder as the ROM's or do I compile the ROM's together to make a .NDS file with them on?
Depends on the emulator and the device being used. For instance, with NES DS, slot-2 Supercard users do not have to prepackage them. Just create an empty nesDS.nds file, launch it, and use the browser to select the .nes file to launch. Slot-1 device users however need to prepackage their roms since NES DS doesn't understand their filesystems, and the resulting file must be less than 3-4 MB or so in order to fit into the DS's RAM. Other emulators may not work the same way. With SnezziDS, you have to preconvert your files, but with SNEmulDS you don't.