Just got a new Drive Shaft, How do I put it in?

Is the driveshaft internally balanced? If it is, then it doesn't matter how you orient it. Any will work just fine.

But if it's externally balanced (a weight will be present on the outside of the shaft, that protrudes out a bit), the weight needs to be in the same place for both driveshafts. The simple way is jack the rear end up only, put one mark on the driveshaft flange & one on the pinion flange with a permenant marker, put a pan underneath the output shaft if the transmission, remove the 4 12mm bolts from the driveshaft/pinion flange with a 12mm 12-point socket, or a 12mm 12 point closed end wrench, slide the DS out of the transmission. Then lay both DS next to each other, and orient them so the weight points the same direction, then make a corresponding mark on the new DS. This will keep the DS balanced with respect to the rest of the drivetrain.

Now reinstall the new DS so the marks line up. If transmission fluid comes out, you will need to jack up the front of the car as well, remove the filler plug, and refill the transmission with ATF until it starts to come out.
Scott