Hi Weiming,
from what you wrote it is hard to say why there is such big difference. It would require to have a look at what you extracted to HL3D.
Regarding the usage of multiple reference layers it is possible to use both (upper and lower) layer in the simulation. During port setup just assign the positive port to the trace, then the negative layer to the lower layer and directly after this another negative port to the upper layer. Should finally look like the screenshot below.
Best regards
Rocco