Looking through the recent issue of Shop Talk, on page 6 I see a photo of the torque wrench being used on the bolt head instead of the nut. I would suggest this is not the best procedure.
Generally I agree with Mike but in this instance it doesn’t matter. Mikes comment, “However, the dominant factor is usually due to the frictional variation that is present between the contact surfaces that are being rotated." says it all.
The tension created in a particular joint is the same whether the tightening torque is applied to the nut or the bolt, provided the element that is driven (nut or bolt) is seated on a similar surface. In other words since you have the same washer under head of the prop bolt and prop nut, it doesn't matter. Some of the studies I have looked at indicate less than ½ of 1 percent difference in torque values.
If you have so much friction in your prop bolts that they will not turn with little effort before tightening, you have a bigger issue that needs to be addressed. The whole torque thing can get confusing and very technical, wet torque or dry torque. Is your torque wrench calibrated?
All that said, I will tighten the nut first if I can.