You are correct in understanding that this is going to depend on the school. The Common Data Set for each university is going to tell you how much emphasis it places on both academic factors (GPA, scores, rank, rigor, etc.) and non academic factors (ECs, LORs, legacy, demonstrated interest, first-generation, etc.). You can find this by googling "name of school Common Data Set" making sure you are looking at the most up to date year (probably 2011-12). You are looking for information on First-time, first-year admission data.
If you have a lower GPA but an upward trend (i.e. 3.0 freshman year, but trending up to a 4.0 your senior year) you are going to fair a lot better then someone with the same GPA who has remained static all four years. What you face with a lower GPA and high scores is being labeled an 'under achiever'. An upward trend in grades can help put that into context, noting a rocky start but a bright and solid showing now and in the future. Also, if you have good EC's schools that use holistic admissions may work in your favor.