Boons are skills your character has access to whether or not they are on the chosen class or general list. If they are already on the general or chosen class list, you can purchase them at a discount. If the skill is not on the chosen class list or general list already, the skill can be purchased for 3 XP. You do not have to purchase these skills now (clicking a checkbox denotes purchasing the skill), they are always available to purchase at a later time if your character has the appropriate XP available.
Please remember you typically have 10 XP to start. You can use the rulebook found here in order to find skill XP values. Your choice of Species and Sub-species should show your access to extra skills or discounts to skills you already have access to