Actually, the only difference between the main login and the portal login is that one is customizable. With your portal login page, you can customize colors and add a logo for branding purposes.
Any user (whether Admin, Agent or User) can log in either of the two ways. Your portal has the ability to match your organizations look and feel.
If you would like more information about your customizable login portal you can find that at Settings > Site settings > Support Portals > Web > Sign Up URL