First, I place nose markers level with the top of the nostril. Facegen is kinda weak making noses but there is a way to get around it.
I have SI Facegen version 3.5.3 build March 2011.
I learned a nice tip that if you morph the actual photo's nose and
nostrils to match SI Facegen's face texture, then paste a cutout of the
photo's morphed nose onto the face texture, blur the edges of the cut
out, make it translucent to match the position of the face textures nose, then get
rid of the translucence, then adjust color and tint and brightness of
the cut out, the nose on the character can be spectacular. Check out
some characters I made for the game Elder Scrolls 4, Oblivion. using an old copy of Windows 2000 Picture It in Windows 10 to do the PhotoShoping of the photo and the face texture:
I
begin by cutting out a copy of the face textures nostrils and pasting
next to the photo's nose to be used as a guide before morphing the shape
of the photo's nose.