There are a number of ways of automatically installing the agent on machines - I'm sure some other posters here can comment on their experiences - but from the ePO side, you can configure an Active Directory sync task to install agents on machines, or you can use Rogue System Detection to do a similar thing. You can always simply send the agent from the console as you have already done, as well.
Outside of ePO you can install the agent via login scripts, for example, or any other method like SMS. If you build machines from an image, you can include an agent in the image (making sure you remove the GUID first) and then every new machine will automatically talk to ePO.
There's lots of options