The .eff files contain the music entries for the zones as well, so those will carry over into the .emt file as you convert them. You'll be able to just change the entry's reference from, say, qeynos.xmi with xmiIndex 3 (pretending that's the theme for the Qeynos Monk guild area) to Qeynos_Monks.mp3 or whatever you'd like to do.
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