Two things I messed up on when I had a long-distance civilian GF (granted that relationship happened when I was in school):
1. Make sure you give your SO a crash course on what your life was like at school and what the Academy is. Most people aren't intimately familiar with the military. They might think you are a normal college student who just wears uniforms, some think you are enlisted and you go to boot camp, and some might even think you just learn how to fight wars. You will undoubtedly be less available (both time-wise and geographically), but with them understanding what you do on a daily basis can help a lot with the inconveniences that you might face.
2. Make sure you both make time for each other. Make sure you are both on the same page regarding that when you schedule time with each other, that time is either honored or you reschedule. You can't just do your own thing 100% of the time (both sides) for an LDR. Spending time with each other is not as simple as seeing each other at school, hanging out on a weekend on a whim, calling each other for hours, etc.
You'll be squawking 7500 for BCT. You are also sort of squawking 7600. Enjoy your last bit of civilian life and you'll be on a discrete beacon code until you leave the service. Then you'll be 1200 again. And that is enough aviation nerdy for this post.