So I've ended up giving up on MameWah - it's turning out to be too much hassle. I've decided on Lemonade for WinUAE - it's really easy to get working with all the games pre-configured (and only one entry per game rather than per release etc.)
Are there any equivalents of Lemonade for other platforms? Basically something that'll just add all the games for that platform automatically, and you just choose them from the list.