Learn about your audience. No matter how well you remember what it was like when you were in sixth grade, researching your audience is important. If you have kids, spend time with them and ask them about their view on the world. If not, use the Internet to research modern middle-school children. Looking at websites for children's TV networks can teach you a lot about the interests of modern sixth-graders.
Work on your protagonist. Your main character has to not only be engaging, they have to be easy to identify with for sixth-graders. The ideal age for the character is the same age as the intended audience or slightly older, so your main character should be around 11 to 13 years old, in the sixth or seventh grade. Most children in sixth grade are developing their identity, and are more internally focused than young-adult readers. Your protagonist needs to grow as your story develops.
Find a way to put your protagonist on his or her own for a lot of the story. Making the characters' parents busy, or otherwise occupied, is a good way of doing this. According to Right Writing, middle-school kids like to read stories where kids their age deal with situations as well as adults. This also ties in to the idea of finding their own identity; as their parents influence fades, they look at the world for themselves and finds out who they are.
Use dialogue. Not only do portions of dialogue break the page up and make it seem more manageable, it is a good way to convey plot-points to the middle-school reader. You can also use dialogue to increase your depth of characterization. Listen to sixth-grade children speaking and note the patterns of speech, topics, vocabulary and grammar. You need to capture the dialogue of sixth-graders to write a believable story.
Use external conflict that mirrors or instigates an internal conflict. Think of a problem to confront your main character with. Think of things that sixth-grade children may experience for themselves. A bully at school, new step-parent or dying family member could present many problems that could cause internal conflict for your character. Whatever the plot for your story is, it is important that the protagonist has a personal choice to make, one that basically asserts what type of person they want to be.