The Regal will have a big engine bracket that cradles the steel oil pan, Bonneville in OP'* year will be aluminum and the motor mount will bolt to it. The oil filter adapter on the Regal pushes straight to the passenger wheel, on the Bonneville it tucks under and cradles the pan.
Regal/Grand Prix/Monte Carlo/Impala
The rear exhaust manifold outlet is typically a little different as well. Regal (aka W body) always has the O2 sensor directly in the way of the #6 plug and the Bonneville will be between #4 and #6.
The coil pack tensioner/bracket will be different between the two as well. And there'* the dogbone mount on the Regal/W body on the driverside that can come off the new motor.
Other than that, I'm not remembering much else. Do a good look over between the two and you'll pick up on any other changes if needed.