Users will be included in the member structure (e.g., matrix plan) if they join for the pay plan. If they only register for the site, their account will not be included in the structure. Please refer to the Payplan Registration Option in the Admin CP, General Settings page, in the Members tab. If you prefer that the system not register members automatically to an existing pay plan, you can select Manual by Member.
For information on pay plan settings, please refer to the online documentation, which includes descriptions and examples, as well as instructions for configuring commissions.