I don't have a clue, maybe Mynex will hop on and tell us where. I know there was documentation on the website beyond a simple FAQ! I just can't find where, maybe there is another PCGen website.
DOH! The pluses on the side can be clicked and you can get more options, but here is what I was talking about
PCGen also includes a Customize function for doing small changes. Just right click on the basic non-magic item in the inventory tab (on the left pane) and click 'Customize'. You can change the size and add simple changes, you can even make a new name for the item. Your new item will then be added to the list for you to buy. But it will only be available for the character you currently have loaded.