After the front flap of the wrap fabric is stapled the whole length of the header rail, you can start wrapping and stapling the back flap completely around the header rail. I like to stop on top and put the staples right in line with the ones underneath, then cut the fabric off just in front of the staples. This is on the top angled surface of the rail that will be just under the outer top fabric when the installation is complete. On my car no one has ever noticed this in years.

But, if you're concerned about minor appearance items you could continue the wrap around and down over the front of the rail and put the staples in front where they would be tightly covered with the final layer of top fabric. A problem you may encounter doing that is that you may end up driving staples into other staples before your done, because there will be a couple more layers of fabric stapled to the front face of the rail.