Schnitz is worried you are going to let your beer get skunky... but you wouldn't do that, would you? Keep those clear bottles stored in a dark place.
When I was bottling I would always use a few clear bottles so I could watch the progress of clearing and sedimentation in the bottles. I kept a few clear 750s and 1/2 liter or 10oz glass Coke bottles for that purpose. Always stored in a closet or covered with something dark and opaque.