First of all, 3s is a bit too low voltage IMO. Even with the two speed, I would shoot for 4s minimum.
But anyway; there is no way to use motor brakes and/or have reverse while retaining the autoshifting two-speed... at least not without pretty much designing a tranny from scratch.
This thread in the Revo section should help you see why this is so. The slayer tranny is close enough to a Revo that the differences are very minor.
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