Manchester is a clockless code, which is why it is used, though you obviously need to determine if there are two transitions or one in a "period".
The picture you show is standard Manchester. I think you are confusing yourself with a differential line signal, which, to software, means absolutely nothing, since your port will only have a single channel, the "BMC" in your diagram, after a line receiver (hardware) converts the electrical signal from differential to single-ended to bring into your processor chip.
At that point, your only task is to determine the shortest pulse width, and from there, you can decipher a change (1) or no change (0) in that period (set up some microcontroller timers to do this for you, or if it's all you are doing and the rate is slow enough, you can do it all in code) and each of your actual decoded bits it 2x your narrowest pulse width.
You have me curious - is that avatar pic before or after the sex change?