One of the main reasons why people (including me) lock the stock tranny into second is to have reverse and use the motor for braking. Because of the way the auto-shifting works, you can't do either of these with the two speed. If you keep the two speed, you would need to retain mechanical brakes (and the extra parts/complexity that involves), and you still won't have reverse.
This thread talks all about the different options for using the stock tranny along with fairly detailed instructions.