The first thing a body loses with the type of exercise routine that you describe is fat. Muscle is far harder to lose than fat, but it can be lost if you're working too hard. Muscle is a much denser tissue than fat. I seriously doubt you're losing muscle. However, your body is undergoing a change of shape due to water loss (temporary) and muscle reshaping of your body contours due to your new routine.
Treadmill (or any) exercise helps your body lose fat FIRST. You're starting the process of firming up of muscles. If you're feeling tired and feel less energy, you obviously need to sleep more and/or change your diet so it includes more calories.
A young teen male in an exercise program should take in around approx 2000-2500 calories per day. When you drop down below a figure of say 1200-1400 calories per day, your body's metabolism can slow down (as though fasting) and it'll start to break down. It sounds as though that's what is occuring, which along with loss of sleep, is robbing you of energy.
However, anyone (including you) is just guessing without knowing your actually caloric intake. I'll bet if you kept a log of calories, you're taking in less than you need ideally to maintain your PROPER weight. I'm guessing that your diet is far too restricitive of calories.
EAT more (adding whatever fun stuff you want to your diet, while avoding white sugar and deep fried foods) to what you've originally listed. Vary your types of exercise and keep at it steadily. Take a day off now and then too. A varied routine of 4-5 workouts per week will help keep you from getting bored and at the same time it'll allow your body proper healing time. Putting 20-30 mins on the treadmill, PLUS around 20 mins on the Bowflex should do the job.