Basically, those rules say that you have a 75% chance of being able to purchase any magic item whose value is lower than the Base Value of the settlement. In addition, the GM rolls up a number of Minor, Medium, and Major magic items as listed on the table, which are also available for purchase. These bonus items must all have a higher value than the settlement's base value.
I'll run through an example, to hopefully make this a little more clear.
Xylitol the Wizard enters the settlement of Sugarfree, a Large Town. He wishes to buy a number of magic items. Specifically, he wants to buy a Potion of Cure Light Wounds, a Headband of Vast Intelligence +2, and a scroll of Magic Missile.
The potion is worth 50 gp, and the scroll is worth 25 gp. Since the Base Value of the settlement is 2000 gp, both of these items are potentially available. Xylitol (or his GM) should make 2 percentile rolls, each with a 75% chance of success. If the first succeeds, then Xylitol can buy the potion. If the second succeeds, then he can buy the scroll. If either fail, then Xylitol cannot purchase the item at this settlement at this time.
The Headband is worth 4000 gp, which is above the settlement's base value. The only way that Xylitol will find this item here is if the GM rolls it up randomly.
At this point, the GM should use the Random Magic Item Generation to roll up 3d4 Minor, 2d4 Medium, and 1d4 Major magic items. If the GM rolls up any items that have a value under 2000 gp (the base value of the settlement), those items should be re-rolled until all of these items are worth more than 2000 gp.
The items that the GM rolled are now available for purchase immediately. If the Headband happened to be on the list of items rolled, then Xylitol can purchase it. Otherwise, he'll have to leave and find a different settlement to buy it at.