Ya - already, anymore (and some more, like "yes", "now" but that's another thing)
Todavía/aún - still, yet
-Ya no me quiere - He doesn't love me anymore
-¿Has ido ya a comprar? - Have you already done the shopping?
-¿Todavía/Aún estás buscándolo? -You're still looking for it?
-Si todavía/aún no lo has hecho no te dará tiempo or No te dará tiempo si no lo has hecho ya/aún. If you haven't finished it yet, you won't be in time.
I think the last one is the only in which are interchangeable. But it's 4:18 here, so wait for some else.