You don't mention which scanner you are programming but I assume you are talking about a 396/996XT. I use Freescan to program multiple sites into systems on my 396XT.
The article in the wiki is more complete than I would be so I'll provide the link to the section on creating sites and then if you have questions come on back. Freescan Create Site - The RadioReference Wiki
This screen can only be accessed after a system has been defined. FreeScan will create a single site along with the system. To define another site within a system, make sure the cursor is on the original site then right click. The screen at right appears. You can also access this form by clicking on the 'new site' button in the toolbar.
ok then this system, I "created looks like the others that I downloaded when clicked on the various sites for some of the systems I created before. I feel so stupid.