Sethumadhavan, just put your photos in a small envelope and label that envelope as "photos" and then paper/binder clip the envelope to the main application along with your check and any other supporting docs. Sometimes you get a semi-transparent envelope in which your passport photos are delivered in ... use that if you get one from the place you take the photos at.
Oh yeah, I just remembered that I used a pen to write on the back of my photos instead, because the pencil was NOT working at all. You think they'll reject the photos?