Which B&M shifter? If it's the Hammer, it's a ratchet type shifter that you can still use as normal in Drive or use the ratchet mode to shift manually through the gears.
B&M's hammer shifter re-centers itself every time you shift.
You push it forward as far as it will go, this ratchets it into the next gear, then it springs back to center position. Repeat as necessary or pull it all the way towards you to go the other way.
Very nice, beats the cheap sounding 'tick' of the stock shifter, plus youll never slam to the wrong gear.
But, to answer your question, the B&M Hammer (ratchet) shifter does not change the way your transmission shifts. It just changes the way you move the gear selector from one position to the next. You would need a manual valve body to change to a totally manual shifting tranny.