Hi Cheece,
Double click on one of the pins on the net tie. Select what layer you want the pad to be on. Do the same for the other pin. You can now pour the planes around the pins. You can leave the silkscreen on the top layer so you know where the tie is after the board has been made. Hope this helps.
You can create the net-tie on the top layer (the SMD pads), place it on the PCB, move the pads to the internal layer and copy/paste that net-tie to the library. It will copy the internal layer as well.
Rename the new net-tie as you wish.