This is the main screen for the Preferences. First thing to look at is Sources.
This screen allows you to select which sources are available to each type.
As an example, here's the Preferences for Armor/Shield Abilities. You put in percent chances for each type as well as values. Here's also where you put in a percent chance for Armor/Shields to be rolled Intelligent.
Here is the Preferences for Art Objects. You can set the percent chances for each level of Art, as well as values.
Here is the Frequencies table. I think I pulled it from an old Monster Manual, but not 100% sure. I added Unique as a 1% chance, just in case you have a named weapon, or something similar. Looking at Minor Shield Abilities, Arrow Catching has a 20% chance to be rolled, while Spell Resistance (13) has a 2% chance of being rolled. It's not exactly the same percent chance as what's in the books, but when you start adding in items from the various splat books, it's the only way I could think of.
Here's the screen for Intelligent items.
Here's the screen for Mundane Items. By default, Hardstones and Shells are not rolled by default, but you can add in a percent chance for them to be rolled.
Here's the screen for rolling treasure. You can
change percent chances to roll any of the types of items for each level.