The reasons I struggled with makeup as a teenager are 1. I bought cheap stuff (not always a problem - I love a good bargain but you have to know what to buy), which led to 2. I hated it looking as if I was wearing makeup, because for some weird reason I thought people would find it funny that I was wearing it or that it would draw more attention to my flaws.
The key, as always with makeup but especially as a tomboy, is subtly enhancing your natural beauty.
1. Key subtle products. Always wear mascara. Use as much or as little as you want, I like to use quite a lot of mascara, but you may want to just simply colour your lashes and add a bit of definition. I've never found that it makes a huge difference which mascara I use (though I have used some bad ones), so something from the drugstore (Boots, Superdrug etc for those of us in the UK) is fine.
Lips - always use a good lip balm. Not only does this keep your lips healthy and looking good, but also adds a bit of shine without being 'too much'. Some good standards are Carmex, Blistex have some nice new flavoured ones out (I just got the Raspberry Lemonade Blast free from their Facebook page and like it), EOS for those in the states (or in the UK you can get it from Amazon). I am an avid lover of the green Vaseline tin that has added aloe vera, and although I've heard that Vaseline is just a shield (still important) and not an actual treatment for your lips, the aloe vera has always helped the condition of my lips. I kept Vaseline in my pocket at school and reapplied frequently. Also experiment with some lipsticks (the Natural Collection ones in Boots are only £1.99 each and shades like Coral Shimmer, Honeysuckle and Sand Castle add a nice subtle 'your lips but better' effect), and lipgloss is always a nice touch as well without looking 'overdone'.
Blusher - now. I've only started wearing blusher in the last week. I kid you not! On Barbara(ThePersianBabe)'s recommendation, I picked up the Natural Collection Blushed Cheeks in Peach Melba, and using a Bourjois Powder Brush I just put swirl a bit on the apples of my cheeks. It's great, because it gives you a nice glow but doesn't look unnatural at all. This is the beauty of blusher - applied correctly in the right shade of course!
2. Hiding flaws - I searched for years for a good concealer when I was a teenager, as I've had lifelong dark circles under my eyes, but didn't find one that worked for me until I was 20 (I gave up on my search and embraced my tired/dead (lol) looking face while I was in school). I found Maybelline's Dream Matte Mouse, and I would highly recommend this as a starting point for someone looking to subtly conceal dark circles and blemishes. The formula's so light that you don't have to worry about putting too much on, and it looks really natural.
I went for a more heavy duty concealer a few months ago, the Collection 2000 Lasting Perfection concealer as recommended by many many YouTube beauty gurus, which is cheap (big thumbs up - I think it costs about £4.19) and really does work. Spend time getting the right shade. Try it on the back of your hand, and even go to Boots/Superdrug armed with cleansing wipes so you can try the products on your face and remove as needed. Picking the right product is key, so always take the time to choose it.
3. Eyebrows - not technically makeup, but still. Tweeze the strays. DON'T GO OVERBOARD, you will regret it. Just keep your brows neat and it won't be obvious that you've tried to do anything overboard. The general concensus is that it's best to get your brows done professionally the first time so you get a good shape you can work with. This sounds like a very good plan to me as so many young clueless teens overtweeze and are dismayed when the hairs don't all grow back, but if you're sensible you can get away with doing it yourself.
4. A bit more daring - try out some nude/neutral/natural hued eyeshadows to add a bit more definition. The Makeup Academy Professional Eyeshadow Palette in Heaven and Earth, available from Superdrug, is only £4, has 12 great natural, neutral brown-hued eyeshadows, most with a little bit of shimmer, and is a good alternative to the much loved but much more expensive Urban Decay Naked Palette. You can apply these with your finger if you like, just to add some colour and bring out your eyes.
As time goes on you can be more adventurous adding in eyeliner, highlighting, contouring, and more dramatic shades. But start at the basics and enhance what you already have.
Let me know in the comments if you want more detail on any of what I've said.