Iris outlines some ways here:
http://utaforum.net/thread-ust-tutorial?pid=30602#pid30602
Another way is to find Nico singer covers - some of them have loud harmonies and that really helps.
But in the end some songs are just really, really, REALLY hard. You know kz(livetune)'s songs? They all have three lines of singing. But you can never hear both of the harmonies (I remember when I tried to do Tell Your World and when I helped Cola do Yellow that the harmonies were insanely hard to pick out even if I'm fairly good at finding them). But for some you just have to try a bunch of methods and you can get it.