Yes, SBA supports different ways to install an Addin but I do not recommend doing anything but installing Addins to the GAC. Why? Because moving forward we want your Addins to work with future versions of SBA, so if you install in the installation directory of SBA 2006 then future versions will not know about this location. So here's my model that an Addin for SBA should follow.
Since I'm recommending to install to the GAC, here is some sample code that shows how to install your Addin programmatically to a company in SBA. The version number and key I got from the properties of the dll itself.
After you install your addin, the next time SBA opens that company, the user gets a dialog informing the user that a new addin has been installed and the can enable them or not. The user has control over what is enabled and what is not and we don't expose this programmatically.