WARNING: You're in for an information dump.
I feel like being a complete and utter creeper for saying this to a teenage girl on the internet, but without pictures of what you define as a "flat" stomach, and being able to see where you're at, it's hard to give precise advice.
In saying that, there are a few things that need addressing here:
1) As a broad generalisation, teenagers tend to have unrealistic standards of beauty. This is typically made out to be a girl issue, but boys are readily prone to it as well. On top of unrealistic standards of what we think we should look like is often an unrealistic perception of what we do look like. When I was a teenager and getting into bodybuilding, I made some alright progress towards that goal (despite being an idiot, which did limit progress a fair amount), but the closer I got to what I considered an ideal physique, the further I felt away from it. If you've ever seen the movie Mean Girls, there's a scene in it in which the popular girls are all standing around in front of a mirror looking for things to complain about with regards to their bodies. When we're trying to conform to a certain image, we have a tendency to do that, and it creates problems that aren't there, and then amplifies them. So it's important to make sure you've got your head in the right place here, in which you love yourself and honour yourself, and make dietary and fitness changes in order to care for your body; rather than running from perceived flaws and grasping at the ever-moving target of "perfection" (and perfection
is a moving target).
2) Now, onto practical fitness-related stuff. I'm going to make the assumption here that "toned" but not "bulky" means you want to look fitter while occupying roughly the same physical space. If it just means occupying less physical space, I'd encourage you to reread point 1, as at 5'08" 125lb your BMI is at the low end of healthy. Now, assuming that I've interpreted your terminology correctly, you would actually get closer to that goal by gaining weight (slowly), because muscle is denser than fat. Usually when people talk about being "toned but not bulky," they're talking about having visible muscle in a balanced manner across their bodies, without being large and without being veiny, "shredded," or gaunt. Due to muscle being denser than fat, thus every pound of muscle occupying less space than a pound of fat, you might be looking at gaining 5-10lb over 3-6 months, and then assessing and adjusting goals from there. That is, of course, assuming I've understood you correctly.
3) I really don't know what people think they mean when they say they want to "lengthen" their muscles, but your muscles are attached to specific points on your bones, and that determines their length. If lengthening refers to having greater flexibility, then the obvious answer is to stretch. If lengthening refers to some aesthetic outcome, then it's probably a misnomer. Could you clarify what you mean by that?
4) Adjusting your body composition ultimately comes down to diet and exercise. That's little d diet, not Capital D Diet (the former being a way of eating, the latter being a way of not eating). I know that you're eating "clean," that you're active most days, and that you play tennis. Without further details, again it'll be hard to give advice and what direction to move in. But I want you to do away with the idea (if it's been implanted in your mind) that there are specific exercises for bulking vs toning. Exercise gives you more strength, speed, endurance, stamina, flexibility or skill. Strength and speed are primarily produced by fast twitch muscle fibers, which are the ones that do the most visible growing. Endurance is primarily performed with slow twitch muscle fibers, which don't do much visible growing. "Toning" generally implies making the fast twitch fibers a little bit bigger and decreasing body fat by a little bit. "Bulking" generally implies making the fast twitch fibers a lot bigger. These two goals are not achieved through vastly different exercise programs; rather, the latter is simply the result of taking the former and amplifying it by dedicating more time and effort and food to the cause. Essentially, this means that once you have all the muscle you want, to avoid getting any bulkier, you simply stop eating enough to get bigger and stop training in such a way as to elicit additional growth; instead eating and training for maintenance, which is achieved through the same activities, but dialled down.
So, whether toning, bulking or maintaining, you would want to do strength-based training to use the fast-twitch muscle fibres. Even though speed training uses those same muscle fibres, it tends not to load them as potently or predictably, so strength-training is more reliable. It's important to keep doing this same type of exercise while maintaining, so that you don't lose what you've developed. I always refer to 6 basic movements to work around, which, put together, work most of the body: deep knee bends, hinges, horizontal pushes, vertical pushes, horizontal pulls and vertical pulls. Here's a simple program I've developed for beginners that operates around these movements, to give you an idea:
http://training.fitness.com/weight-training/basic-novice-program-strength-muscle-54545.html
