Each cable runs through its own tube, so they can't even cross until they exit their respective tubes, which is only about a foot from your access panel at the very front. As stated, you can snap a pic with your cell phone and make sure they are parallel and not crossed.
I'll let others chime in to correct me if there is a better way, but you will have to feed the clutch cable(fat black end) back through the engine bar hole first past the cylindrical grommet attached to it, then push the front of the cable into the tube. This will hopefully make sense and is probably obvious to most.
This is because the cable housing fitting that mates to the end of the clutch tube itself won't fit through the engine bar hole. Simply put, you can't just thread the front end through the bar and into the tube as might be your first inclination. I attached a another pic of the inside front of the tunnel for viewing pleasure. Sorry if the pic ends up sideways.
Click to view attachment...couple more pics of where the clutch cable goes thru the bar and mates up with the tube...excuse the tie wraps...they are currently "place holders" as I haven't hooked up the pulley end yet.
Click to view attachmentClick to view attachmentClick to view attachment