This is what I did. My undergraduate GPA was awful, but I knew of a program that would let me go for my MS. I finished it with a 3.9 GPA and the acceptances for my PhD applications rolled in (I still addressed my low GPA in my SoP, as previous posters have also suggested). I used the same logic. I figured that if I proved I could finish an MS, then that would demonstrate that there is a good (or, at least, a better) chance of finishing a PhD program.