To be honest, I'm not sure exactly how it would work within a mame list, since rom list generation can be built a few different ways depending on how you like it.
For instance, my mame roms have the basic mame shorthand naming convention, so something like "Bloody Roar 2" is reduced to bldyror2. Then, the list generation method in my mamewah (v 1.619b) has rom_folder_vs_list_xml, which then 'converts' all the rom names into the full names noted within Mame and the mame.dat files, etc. So this means if you pop in a rom that's not in Mame, it probably won't get populated on the list, and therefore you won't even get it to show up.
By using a game specific INI file, you can basically tell Mamewah "Use the basic setting for all these games, but for <gamename>, use these settings instead." Since Zinc emulates a few games that Mame does (and much faster, at that), you can make ini's just for those games, and tell mamewah to use a separate emulator for them. Since the games are already in the list, they'll populate correctly when you generate a game list. Since you're wanting to have all games in one list, and because Mamewah generates lists for Mame in a non-standard manner, I think you'd be better off having a "mame" list and an "others" list.
This might help explain a bit... For just about everything *but* mame, I have the romlists generated through the 'rom_folder' option, which means anything in my rom folder with the right extension gets shown in the gamelist. What I did was put all my sonic games into a separate folder, and 'pretended' they were all Genesis games, setting up my ini settings for using my genesis emulator. For the games that were on non-genesis hardware, I put in those 'game specific INI' files just for them, which basically told Mamewah to use a different command line (and therefore, different emulators) to run those specific games. End result is that I have one uniform list of games that are 'themed', and although run on totally different emulators, it's transparent to the user and the games just run when played.
As for the separate lists, My setup has 2 buttons that are used to 'flip' through the various emulators/lists on the cabinet. My layout also has arrows and the buttons needed to flip. I'm thinking that you could possibly get away with having just two lists, and as long as you name them something self-explanatory, you could get away with people not being too confused.
For instance...
"Arcade" for mame list and "Toasty's Top Picks" for secondary list.
"Mame" and "<street name> Specials"
etc etc etc
I think the main problem here is the way that mamewah generates the romlist for mame.
Anybody else have any ideas?