I'm doing lots of bird photography lately with my d7100 and my AF is missing more of the shots than not. I'm wondering if there are any rule of thumbs or techniques i'm not aware of that could help me to use my AF system better?
It would help to see what your problems are.
Normally, AF will tend to focus on the object nearest to the lens. If you are shooting photos of birds sitting on a tree branch, the camera will almost always select the smaller branches in front of the bird as the object of interest.
Since you are normally focusing at a greater distance from the subject to the lens, even the higher aperture value of a zoom lens tends to create an image with the bird slightly out of focus.
More focus points will be the wrong approach as it will simply add more possible subjects to the frame. Narrowing down your selection or moving the AF point manually is typically a good idea for a roosting bird. Unfortunately, many of your opportunities will literally fly away by the time you've adjusted your camera.
One of the skills you will need to develop to be successful at birding is to anticipate a shot by predicting the activity of the subject. Not always easy to do, particularly if you do not have the fastest lens with the quickest focusing system.
Since this forum doesn't have a dedicated section for such photography, look through the threads found here;
Nature and Wildlife Photography Forum: Digital Photography Review
You can also move up to the "Canon Powershot" section of the same forum. The Canon SX series was a very popular camera for wildlife birding and the subject is covered in several threads there.
You'll have to look through the threads. This subject comes up on occasion.
There was also a recent thread on this forum asking for reference material for birding photography. Tony Brittton gave a very good suggestion of a reference book.
You might also find some useful tips on this site;
Backyard Birding with Kenn & Temple
Capturing birds in flight is a totally different issue.
Show us some photos.