Everything will revolve around the Clients part of the system, even if you are a single user or single limited company.
Here you can create your Client's account, attach the governments HMRC gateway information, create the required security tokens and then go on to Authorise and submit the likes of your Vat Returns.
NOTE
If you are an AGENT then you will add in (x) number of clients that you are acting on behalf of. You will need to be licensed for the correct number of clients !