MAME looks for the zip in the root of roms , then looks for a matching subfolder with the CHD inside. If the CHD is in the wrong place, you will get a fatal error.

You must have the naomi.zip BIOS file in your ROMs folder, or the emulator won't know how to "talk" to the virtual arcade board. How to Set Up Your CHD Folders

To successfully emulate Marvel vs. Capcom 2, you must understand how MAME handles complex arcade hardware. Unlike older cartridge-based games (like Street Fighter II ), newer arcade systems used hard drives, laserdiscs, or CD/GD-ROMs to store massive amounts of game data, such as high-quality audio, 3D textures, and cinematic videos.