Marking it always has worked for me. You can use white out, or you can take a center punch and ding the very end of the pinion shaft, and then right across from it put a ding on the nut. It's just a reference to get you back in the ballpark.
The most difficult part is loosening and then tightening the nut if you are doing it by hand, it's very tight. You usually need a cheater bar to get enough torque to get it loose. To get enough room to swing a cheater bar, you need to jack up the rear of the truck off the ground. But then when you do that, there is nothing to hold the rearend from turning. The parking brake won't do it. What I did once was get a thick piece of flat metal, and drilled two holes in the end to line up with the holes in the yoke. And then temp bolted this flat metal to the yoke, and let it swing around and hit the ground. That would hold it while I took the breaker bar with the cheater on it and broke the pinion nut loose. I have a impact gun now, so it's much easier to use it.