Probably the best thing to do is to copy someone who has achieved what you are trying to achieve. In other words: a powerlifter trying to keep within a weight class. A powerlifter is someone who trains for strength and not appearance, as opposed to a bodybuilder.
If you want to train for strength and not size then train like a powerlifter, with lower reps (<6).
Many people have a hard time putting on muscle, especially skinny people. Most of the time, the problem is that they don't eat enough, and I've heard time and time again people finally putting on muscle after they upped the calories that they couldn't before. I know you actually want this - but I am just saying this to prove that your body can't put on muscle if it doesn't get enough resources (food). So just don't eat masses of food and you won't put on much muscle, especially if you are naturally skinny. You'll still gain strength, because your body will become more efficient and your nervous system will get stronger. This is what powerlifters do when they don't want to gain weight, I think.
Strength is different to endurance. Lower reps usually lead to the fastest strength increases, while higher reps (20+) leads to endurance. Plus, 20+ reps won't build muscle very well.
You will probably lose flexibility if you work out without stretching, so do them.
If you want a strength routine look for a powerlifting routine. Look at websites like
www.exrx.net for exercises. Usually the heavier you can go on an exercise the better the exercise is. (It is better to do a simple curl movement for biceps then some weird movement that you can't do much weight on, for example...)
By the way, I don't believe it is possible to tone muscle like Martian seemed to suggest. Most experienced lifters believe it is a myth. Muscles look tone when there isn't much fat covering them (maybe this is what he meant?).