If you haven't gotten any of the holes for the Utilitrak drilled yet, I'd spray first and then drill the holes for the trak. I can't imagine any problems drilling thru the bedliner and the bedliner will be adding thickness to the bed (about .125") so drilling after would be better in my opinion.
If the holes are already drilled, just make sure to cover them up or put screws/paper in each of the holes so the bedliner doesn't get into the holes.
If the holes are already drilled, just make sure to cover them up or put screws/paper in each of the holes so the bedliner doesn't get into the holes.