I love working cardio with my weight training. Cross training provides a very synergistic effect for performance both in the weight room and on the track.
The stronger your legs, core etc are the better your performance will be running a track, bleachers, jump ropes etc. Squats are a great way to build your legs and core as are deadlifts and many other lifts.
The better you perform on a track the more your body is primed to utilize oxygen in physically demanding situations which translates to better lifting sessions in the gym as your muscles will not fatigue as easily, allowing you to lift more and for longer amounts of time which of course produces growth in strength and size.
If you are concerned about calories, treat cardio nutritionally as you do a weight session. Have a pre-cardio meal, look at runnersworld.com for some good ideas (after all they are the running experts) and have a post meal. Up the protein recommendations they offer as building muscle is your goal (post meal. you don't want heavy stuff in your stomach while running, jumping etc), but do take their carb recommendations for what they are.
If you find that you are losing weight after awhile, increase your caloric intake.
At first your lifts will seem to suffer. This is because you are making more demands on your relatively out of shape body. Once it adjusts to the running and lifting, you'll be back to normal in the weight room and better on the track as well as a better all around athlete with a better all around body.