If you want to gain mass and strength you should do around 2-3 sets of 10-12 reps

To increase your maximum strength and power, you should do 1 or 2 sets of 3-6 reps.

As far as the weight you should use is concerned; The last couple reps of each set should leave you temporarily fatigued. On the last set, you should go until you fail to complete another rep. If you can do more than the said amount of reps, increase the weight a bit.

I would recommend using each method above, switching every week. Periodizing has been proven to get better results.

Remember to give your muscles time to recover, too. If you over work them, your risk for injury is high, and your results will be negated. 24-48 hours recovery time is a good rule to follow.

Also, if you run as much as you said, try to do that before the squats. Running when your legs are already fatigued is risky.
It’s also good to incorporate some other leg exercises like lunges to keep your muscles guessing. You should also do some dead lifts, or leg curls to train your hamstrings. If you just train your quads, you’ll get a muscular imbalance, which leads to injury.

I can’t tell you how long it will take to see results because everyone is different. I can say that if you are disciplined, and dedicated it won’t take that long.

I hope that covers everything, and helps. Don’t be afraid to e-Mail me if you want more specific recommendations.