You use AGENT if you are exactly that, you prepare accounts for your customers, you do work on their behalf and you submit the likes of the Vat Returns for them.
So, pick this option if you DO NOT WORK for them directly but are acting on their behalf as their AGENT.
HMRC have said that they will be implementing the true requirements for AGENTS, so rather than you having to have all your customers gateway details and passwords, the system will be set up that you simply Request Agent Authorisation on behalf of the third party.
So your own HMRC credentials will be automatically linked to those companies / etc that you can act on behalf off.
NOTE:
Do not use this option if you are employed as an accountant and are responsible for submitting multiple returns for numerous companies within a group as it were.
If you are unsure please ring support on 0161 660 1366 or 0151 905 5695