If you're speaking the truth, I know how you feel. I sucked in high school, but because I was extremely bored. Most honors level classes didn't require much work for me, but I still did well. Some subjects I was bored out of my skull, and those I typically didn't fare too well. Now I have the focus to succeed no matter how matter how boring the subject.
In all honesty, it will hinder you some. The higher focus of scrutiny is A school and NPS grades, as well as ACT/SAT. You can do a few things that will make your application very impressive though. In all courses, kick ass and take names. Do your absolute best to do well. Try to get into leadership roles every chance you can, including community service. It will be awhile before you will be able to apply for the program, so you'll have more time to better yourself. Prove yourself worthy while in the Navy, and your past performance in school won't look as bad.
These are just a few things, but they are good places to start. If you don't become an officer, you'll be a better person and sailor either way. The best thing I learned was how to push myself to succeed. Best of luck to you.