The FAQ on Medifast's official website is awesome for these kinds of questions. I know, because I'm new, too - and I was hopping on the web checking my questions about ten times a day when I first heard of the program.
What I've read is that - if you're currently exercising regularly, they suggest you cut that routine in half for the first few weeks of the program so you're body can adjust to the low amount of calories you're taking in. Once you've let your body adjust, you can up the time and intensity - they just tell you to be aware of your body and not to push yourself too hard. I don't personally have any experience with this, but that's what Medifast says!
I figure that you could do the typical 5 and 1 diet, but instead of using the 55 shakes, use the 70 shakes. The 70 shakes have about 3 mg more of protein, and 10 calories more apiece - they're "recommended for men and for women who are active or prefer a higher protein count". I'm not sure how it effects your weight-loss, if at all, but I'm sure some of the veterans on here could tell you.
I worried about the same thing when I was doing my research on Medifast. A lot of people end up gaining weight back. But at the same time there are a lot of people who successfully, and permanently, lose weight using the program. I think that what it really comes down to is you. I hear a lot of people say - this isn't just a diet, it's a lifestyle change. And it really is. Medifast is a tool that can help you to become a healthy, happy person. If you look at it as a quick-fix, that's all it will be. I wouldn't be trying Medifast if I wasn't 100% sure that I am dedicated to making a lifelong change, and I think going in with that frame of mind is really the first step to succeeding in the long run on a program like this.
In any case, I'm sure you'll find the perfect way to personalize Medifast according to your needs. And good luck!