Your situation is very common. This is why, when I taught second-year CCD, I always called it that: second year, not second grade. It was fairly common to have two or three third graders in a class of 12-15. Over the course of several years, there weren’t any problems. If there are, let the teacher know that it is a sensitive subject for him, and that you’re trying to keep his experience in CCD positive. But by all means, even if there don’t happen to be any older kids in your son’s class, do assure him that, “A lady who teaches CCD told me that this happens all of the time, and the older kids often make some of the best students. It isn’t when you start, it is how you do it that counts.”
It is also common for the First Reconcilliation and First Holy Communion time to become a sort of a revival time in the domestic church. By all means, pursue that! It can pay such huge and lasting dividends.
The time of preparation for First Reconcilliation and First Holy Communion is an excellent time to increase your devotion to the Mass and to the sacraments. If it has been awhile, start with reading the applicable sections from the Compendium of the Catechism of the Catholic Church or from the *Catechism *itself. Both can be downloaded for free from online from the Vatican web site. (I usually just cut-and-paste the sections of interest into a Word document.) There are other apostolic letters on the Eucharist that are very inspiring, too.
This is also an excellent time to find somewhere near you for Eucharistic Adoration and a great time to start going to confession regularly–our pastor recommends once during Advent and Lent as a minimum, with the ideal more like once every month or every two to three weeks. Regular examination of conscience (preferably daily) and confession are irreplaceable in formation of conscience. Your child can memorize the commandments and the precepts of the Church, but it is the application that changes one’s life. By all means, start availing yourself of both the Eucharist and confession on a regular basis, with the plan of making these a regular part of your child’s life, too.
If your son is behind on learning the prayers, the best way to learn them is to just pray them on a regular basis.