When you drive, some will go up the tubes in some axles and stay there, so after you drive a bit go back and check the level. The other option is to jack up the truck from one side of the axle and let oil run down to the opposite hub. Then jack the other side, let the oil settle a while and recheck. I do this after I've rebuilt an axle to make sure the bearings have been lubed well.
As to six quarts vs five, I know I would NOT fill over the upper line on the dipstick. In fact, I have always been skeptical of Jerry's (the owner and engineer at Mag-Hytec) stance on the oil levels. I have had it pounded into my head by various engineering contacts that an overfull diff is bad news. I have to revisit this with some of them when I get a chance. Like 2010_FX4, I hedged my bets and didn't go to the full mark. Even at that the oil level is about 3/4 inch above the factory fill line and oil is flowing freely up the tubes. That part might be a good thing in terms of wheel bearing life but my biggest worry is oil foaming/aeration... something that increases the oxidation rate of the oil. When you talk to Jerry, he makes a good case and claims to have thoroughly tested his method. He COULD be right but it's not proven to my satisfaction. Anecdotally, I have thousands of miles in two trucks with the diffs ostensibly "overfull" and nothing untoward has happened. I guess my research could be said to be "ongoing."