When you fill out the online application they ask for all of your grades. You end up with an overall average GPA (combining undergrad and grad). They also figure science and non-science GPAs. There is a GPA listing for undergrad vs. grad, but since your grad is higher it looks good for you.
I think that each school looks at this differently. Is your grad degree in a science? Or a medical area? This is probably most helpful, but even if it is in something else the fact that you have completed a graduate program with flying colors will help you a lot. Play it up!
Don't worry yet about your MCAT score. I've known a number of people who have been convinced that they have bombed it and then ended up with 27+. Of course, doesn't work out for everyone, but you really don't know until you get the score in hand.
Other things to consider...Be sure you spend some time shadowing physicians (preferably DOs). Even single days are better than nothing (find a place to mention your shadowing on your app...I fit it in on my secondary). Also, play up your work experience (how you are *more mature* now, how your previous experiences can help you be a better physician, etc.). If you don't have a DO that knows you well, work on that now so that you can have a good DO letter for your app.
Good luck!