We registered a site and domain with you for six years (it's about 3 years old) and I do not show the domain name in my classnames.net account. It does show that I own it when I do a whois search and it shows that it expires in 2015 but why wouldn't it appear in my classnames account as a domain I own?

Also, we are starting another site for another reunion and one of the committee members already registered a domain name through godaddy for something like 7 years. If we transfer it to you guys what happens to all those years and what is the cost to transfer?

There is no need to transfer the domain name. She can keep it at Go Daddy, but just change the A RECORD at Go Daddy so it points to your new website.

Tell her/him to follow these instructions:
If you wish to point your domain name directly to your Class Creator web site, please go into your domain manager at your existing Registrar and add the following IP address to the A record: 69.41.171.62. This will link your domain name to your Class Creator web site. If you need assistance please call your Registrar by phone and read them the above instructions and they will be able to assist you. Please note that the ONLY thing you need to change at your Registrar is your A record. You do not need to change anything else, such as nameservers. After you've done this log into your class web site, click the "Register Domain" link, and type in your domain name and then click the Activate Domain Name button. This will link up your domain name from your Registrar to your Class Creator web site and you'll be all set.