Right now, music is really the only career I am seriously thinking about. But, I can only play the flute and saxophone at an okay-ish level and only know the very basics of music history and theory. I am 200% certain that this is not enough to get accepted into any sort of college. Are there any courses I can take in high school to help with this, or any good books, or websites? I don't have any checkpoints as to where I need to be or what I should expect to have to know at all. This isn't very urgent, since I won't even be in high school for a year at least, but I would still like to know.
I am 200% certain that this is not enough to get accepted into any sort of college.
I am 100% it is enough!
Although it may be different in different countries, music schools in the US are pretty much exclusively interested in the talents you show in your major. If you are applying for music performance, they are interested in your instrumental abilities. If you are applying for music composition, they are interested in your compositions.
Some schools will give various placement tests (usually music theory) during audition weekends, but only rarely do these tests actually factor into your acceptance.
The well-rounded education in music theory, aural skills, music history, keyboard skills, etc. is something you will get as a part of your degree. You're welcome to practice/study these things now---and if you high schools offers theory courses, take them!---but it's not a requirement to get into a college.
With that said, if I could give one piece of advice to someone your age considering a career in music: Take piano lessons. Piano lessons will give you a wonderful background that will help in your later theory courses, and they will save you money by preventing you from having to take some (or all) of the required keyboard courses.
I am 200% certain that this is not enough
I can agree 100% with Richard that not only are you on track, you may even be ahead of the curve. Not getting into a prestigious private conservatory is one thing, but there's a wide range of options and you have plenty of time.
Are there any courses I can take in high school to help with this, or any good books, or websites?
Take whatever your school has. Join the band/orchestra/jazz band/choir, whatever they have. If they don't have it, see if you can do some kind of independent study. Though it was many years ago and every school is different, I was able to replace all my "study halls" with "independent music study" where I could find a corner in the music department and practice or work on things the music teacher would give me.
Get a method book or series of them for your instrument(s) and get a theory book. Work through them at your own pace, there's no hurry.
I could give one piece of advice to someone your age considering a career in music: Take piano lessons
And I also agree with Richard about piano. It's the common tongue and you'll probably be required to take piano anyway so you might as well start learning now. You don't need to be a virtuoso or anything, you just need some basic competence.
Lastly, when you get closer to applying/deciding, try to talk to an advisor or somebody at the school. Every school is different and will have different expectations. I was able to get some advice on exactly what I had to brush up on to get in.
It seems you have plenty of time, so keep going with flute and sax(es), and add clarinet to your list - a not-so-bad transition from what you already play.
As previously mentioned, piano is a must. Partially as it sets out things quite graphically, thus making theory more easily understandable.
It's not a bad move to go through the exams of a local or national board - don't know about U.S., but in doing so, there'll be structure to your learning, at the higher grades playing will help with theory, and vice versa, and you'll have some certificates to wave at the interview. Level of playing for entry to College/Uni is probably about the same as in U.K., where grade VII/VIII gives you a good chance of acceptance. A dip would be even better, and attainable with enough time - and talent - and maybe a teacher...
What musical job do you see yourself doing, a few years after college? If as a performer of flute/sax, I'd expect you to be rather more than 'okay-ish' now. Start practicing - hard! For general musical training, you ask about high school courses - well, what does the music department of YOUR high school say? If you're doing more than vague dreaming, any music teacher will be delighted to help you and point you toward what's available, in or out of school. Start tomorrow!