This is what happens when marketing has say to what is in the manual. There is no such thing as "Hall sensor mode"; there are input capture, output compare and times can be chained as master/slave. Oh and there's a marginal feature, which XORs together 3 input channels; I'm not quite sure why would that be useful but I don't do motor control.
Define in timing terms, what do you want to achieve (draw a timing diagram) and write your program accordingly.
JW
