A long distance relationship presents some unique challenges. That doesn't mean they can't be awesome (I have done it).
Some of what you wrote, being worried about whether you are making your partner happy, aren't only part of a ldr. Every relationship has these issues... Being able to be physically close does make it easier.
I have two pieces of advice.
1. Acknowledge that an LDR is challenging. You are to feel insecure at times... accept it and deal with it. Be open with your partner about how you feel and what you need to feel more secure.
2. Do all the things you would do to have a normal healthy relationship. Talk to your partner daily. Tell him what you appreciate about him. Tell him what you need. Listen to him about what he needs.
Great relationships are built on communication. In the age of Skype, you can make this work.