What is improper use of the Realine trays?
Answer: Improper use of the trays is, for instance, being lazy and wearing the trays only at night. Or, using them as a bookmark in your textbook. Or, life sometimes gets in the way: a legitimate emergency may interfere with your progress. There are other examples of improper use, but basically, if you are not exactly complying with the instructions for use of the Realine system, that's improper use of the trays and you are not going to get your predicted results.
You can still get those results, but extra work will be required, and there will be additional fees. Rest assured, Dr. Meyer is not going to leave you hanging. One way or another, you will get the best results possible. Be compliant and follow the instructions, including the brushing and flossing instructions, and you will get the best results possible. (Worth mentioning here: Long term success requires retainers, which is addressed in a different question.)