I cannot stress the importance of applying early(even though this has been beaten to death). While applying I realized my gpas were pretty low for allopathic schools so I tacked on a couple of DO schools as well to get all my bases covered. Until I got my interviews I tried to down play my gpa and stress my MCAT and extracurriculars. Afterwards I included the factors contributing and how I had fixed those issues during undergrad (upward trend etc) in all my letters of interest.