Just leave Yloc=0 unless you have a compelling reason.
It works better for thin-surface aero to have the wing connect through the center line.
Thick-surface aero does appropriate trimming.
Leaving Yloc=0 makes it easier to deal with parametric changes later -- if you have a tapered fuselage and move the wing fore/aft, or if you change the fuselage diameter, or whatever, you don't have to come back and tweak or adjust the wing's YLoc.
If you fine tune the YLoc to just barely bury the root of the wing to the fuselage, then you've created an overall system that is fragile to parametric variations. However, if you just bury the wing to YLoc=0, it is much more robust to later parametric variations.
Rob