Generally I don't prescribe distance running for people who are trying to lose weight and improve their fitness, as interval training is far safer and effective. Since you have a specific goal in mind (to run a marathon), you will of course need to get some miles under your belt, and you should do it in a gradual fashion. Start slowly with shorter distances, and do a longer run about once a week. As you build up, you can increase your distance. Running intervals will help too - sprinting for small distances, then jogging for longer intervals.

In addition to the long cardio (running, cycling, etc.) I highly encourage you to take up some form of weight training. Increasing your strength will actually help your stamina on the runs, since it has been shown that anaerobic exercise (i.e. lifting weights) has aerobic benefits. Fitness is more than just having a certain body composition or being able to run long distances - it also demands good strength, proper flexibility, balance, agility, power and explosiveness, speed and endurance. Focus on whole body exercises (squats, deadlifts, presses) and on building overall, functional strength. A good trainer will be able to help you put together some sort of program.

I like to think that being an exercise generalist is far superior to being a specialist. You can still work towards those marathon goals as long as you balance your fitness skills.

Finally, make sure you are taking a quality fish oil supplement (liquid) each day, and a good multivitamin.