Hey, LittleBlackStar! Others have mentioned great ways to get started with makeup so I won't go into detail on that, but I do want to address some things you brought up. It sounds like you don't feel comfortable to be yourself at school. Once you really get started with makeup, you're probably going to want to try out some more bold looks that will be noticeable, and it might feel awkward and stifling to not be allowed to do that among your peers. You may even feel like you have to wear clothes that don't suit you and to keep your hair short. That sucks! So I hope that you have supportive people in your life who can guide you through this process.
1) Many communities have LGBTQIA organizations that support non-gender-conforming teens. I used to volunteer at a youth lounge which was one of the few places in town where some of the teens who came felt really comfortable to be themselves. Sometimes they'd even bring clothes to change into that they felt they couldn't wear at school. If you can find a place like this, you'll at least have one place where you can be totally comfortable in your own skin.
2) Hopefully you have at least one friend, parent, relative, teacher, or other trusted person who you can talk to about this. I'm not going to pry and ask a lot of questions, but I'm guessing that you are either interested in cross-dressing (maybe just part-time) or in a full male-to-female transition. Either way, there are people who can help you through this, and it's great if you can reach out to them! An LGBTQIA center is a great place to start, but you'll want to tell other people eventually, too - even your doctor if you think you may be trans.
3) Eventually you may want to come out so that you feel free to wear noticeable makeup at school and change your hair and clothes to something you're more comfortable with. You might want to change your gender pronoun to a feminine or gender-neutral one. Nothing about this process is easy, but from what I hear, it's totally worth it so that you don't have to hide a major part of yourself. You may think you're the only one going through this, but you probably already know people going through similar experiences - you might be happily surprised when you reach out. Obviously, you know what your community's like and you'll know best whether this can be a quick, easy process or whether you'll need to take a lot of precautions.
Sorry if I'm being extremely presumptuous, but nobody else brought this stuff up so I wanted to chime in. Feel free to PM me if you want specific resources, and best of luck with the world of makeup! It's a lot of fun.