I try to match up the carb to the fuel tank location, along the center line. Whether you use the top of the engine bearers or the bottom is really immaterial as it works either way well. But the engine has to match up with the front of the plane and the center line for the fuel tank as much as possible.  A lot of the RC combat guys mount the engine upright on the bottom of the engine bearers as it just seems more natural to do so.
Now there are a few engine designs that don't have as much room on top of the engine lugs for mounting on the bottom like that, but those are the exception.