Make sure BD is set to work with MIDI and click on Bar|Beat marker generation. I always work in region view.
- Tab to the first note
- Trim region start to this note
- Place the region on any bar (lets say bar 10)
- Start playback from that bar, and count along. I do it in chunks, so I'd probably hit the up arrow right before I've played two full bars.
- Shift-Tab to make the selection 2 bars exactly
- In BD, hit Capture selection, and visually check that the selection end shows 12. If not, type it in.
- Hit Generate, and choose to Preserve sample position.
Now BD has created a correct tempo map for those two bars, and you just continue in the same way throughout the track.