trouble win rigify

I am attempting to rig a character with rigify.  I have placed all the bones in multiple different ways by rotating , scaling and grabbing.  However when the rig is generated the arrows pointing down from the hip are rotated apron 90 degrees so the knee deforms laterally instead of in front.  I have rotated the pole vector but that twists and deforms the mesh. If i add the rig and generate without any adjustment the knee moves in the proper direction, but since the rig is not really lined up it has less than perfect results. Any assistance would be greatly appreciated