I think in a certain sense, it's the same as learning any other type of music: you have to have a clear idea of what's going on, how the piece is put together, etc. The difference for me is that while you can fairly take it for granted that Brahms, Schumann, Chopin, Liszt, etc. are going to be mostly pianistic . . . it's not necessarily so for the thornier, more avant-garde stuff. In the case of folks like Ligeti, there are some somewhat uncommon things you have to wrap your mind around in the score before knowing how to practice (unusual uses of bar lines, varying time signatures, multiple staves, etc.). . .
My best advice for any of this stuff (I'm including the virtually the whole tent . . . Debussy, Bartók, Ligeti, Carter, etc.) is to play through it in small portions and very slowly; and also, to spend some time with it away from the piano. The slow practice at the beginning is not for getting it into your fingers - it's for getting it into your ear. Incidentally, when I do this, I find that fingerings and choreography suggest themselves as I go (obviously, they have to be checked at tempo, but it's helpful nonetheless).
Although listening to recordings can be tempting (and helpful at the right stage), again I think there's nothing more useful for wrapping your ears around it than playing through it slowly a couple times (listening to different parts as you go) before beginning work in earnest.