The Environment Variable configuration means that you want to configure your variable(s) in the SSIS Package to take the value from an Environment Variable. Environment Variables are set at the Computer / Server / System level.
For example, you could store the connection string for a database in an environment variable and configure all your package that run on that server, and use that database, to take the connection string value from that variable.
Same with Registry Configuration setting, where you have Registry keys that contain your SSIS variable values.
See the following MSDN Article for detailed explanation on all the configuration types.
I know SSIS tends to be a little confusing when you get started :) I went through the same issues.