I always once a week do a squat variation. Especially the front squat with how it engages the core, more emphasis on the quads and like how Alan said it is a self correcting exercise.
On RDLs and other accessory exercises, you can do them. But as a beginner you don't need to do too much other than your main lifts.
On percent of weight you should do. First, never go to failure. It is better to do half the reps with a weight than to go to failure i.e. if you can do 10 reps with a certain weight, but the last 2 reps are a real struggle, just do 5 reps. It's like a track session you never do intervals to failure. You always(or at least you should) leave room in the tank where you know you could easily do a few more.
On how to do the reps: Focus on exploding through the rep. And,if you're deadlift don't bounce it. It's called a deadlift, lift a dead weight. No bouncing. Also, pause reps on other movements is a excellent way to prevent cheating and bouncing the weight. For example, if you bench pause for a moment at the bottom than explode through the rep.
How often should you lift? Depends, in the off season about three times a week. During the season just once or twice.
Also, I agree with Alan on upper body movements. Your a distance runner, so you don't need too much. Just enough for balance. So, just a few chin ups, overhead and dips is about all you need.