Muscle building can be useful for weight loss. Experts disagree, but a pound of muscle is generally said to burn between 13 and 25 calories a day, and no doubt it varies from individual to individual. A leg workout is going to improve your muscle mass significantly, both in your legs and over the rest of your body, because of the hormones excreted during strenuous exercise of large muscle groups. Muscle building is an incremental way to burn calories, and you have to be careful not to increase the amount you are eating, but it does work.
Bigger muscles are not going to significantly effect your ability to run. They aren't going to hinder you, but leg exercises such as squats or calf raises build up fast-twitch muscle fibers. Running uses your slow-twitch fibers instead, which burn more calories and take up less space, as well as lose endurance more slowly.
Running is a mental thing more than a physical thing. Turn on the television and find a show that you like and can focus on while you are on the treadmill, and you'll notice that you can run farther, faster. Once you've 'explained' to your body that you intend to run a few miles every day, it will stop complaining quite so much. The trick is just to keep at it, and push your boundaries. Set a goal and reach it every day, and push it just a little farther every time you get on the treadmill.
http://www.fitresolution.com has a great feature that lets you set a goal for miles run in a week, and then tracks your progress as you log workouts. The site is completely free, and it's a great way to keep track of how you are doing. They've also got some great guides. An excellent weight loss guide can be found here: http://www.fitresolution.com/guides.html?guideid=17
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