If you would like to add an agent to a group you may do so using the Atomicorp GUI or using the terminal.
Adding and Agent to a Group in the GUI
Under the current group, (default isuse the selection box located to the right of the agent to select the agent(s) that you would like to move. Once selected, look to the bar above and you will see <assign selected> and <apply>. Click <apply> 
In the new window that opens, under the <New Group> selection box, click the drop down and choose the group you want to move to and then click <save> at the top of the selection screen
Adding an Agent to a Group in a Linux Terminal
As root run
/var/ossec/bin/agent_groups -a -i <agent_number> -g <group_name>
You will be prompted y/N
After selecting 'y' your changes will be confirmed