Actually, FreePBX does not use agents.conf at all. The deviceanduser setting is a FreePBX configuration that is different.
It is possible to manually create agents.conf files and use agents in FreePBX queues, you can hover over the tooltip for static agents to see more info. However, there are known issues in FreePBX when doing this. It is not technically a supported setup but it is possible.
you need to change the setting in FreePBX from extensions to deviceanduser mode. You will find this in the amportal.conf file once it is changed you will need to restart asterisk. It will then generate the agents.conf file.