When a player learns a magic skill (other than a Gateway skill), they learn one magical ability of that type, and must describe exactly how it works. All magical abilities are subject to GM approval, and the GM may want to provide examples of acceptable powers. If a player wants to use more than one similar ability, they can take the Extra Magic Ability feature so that their skill can have more than one function.
The player and the GM should also work out when the ability requires a roll and/or what the skill level means in terms of how good you are at this magical ability. Whenever a roll seems necessary, you roll with that magical skill. For example, if your game has a skill called Fire Magic and your character uses it to hurl fireballs, then your roll to see if you hit the bad guy with a fireball should be with the Fire Magic skill.
Basically, each magic skill you put xp into can do one thing, and you choose what that one thing is when you first start spending. If you want your magic to be able to do more things, then you can get the Extra Magic Ability feature. If you do, then both of your abilities use that same skill check.
Example
Suppose Maylene puts xp into Command of Animals. She decides that she wants the ability to sense the emotions of animals. She spends points until she has a skill level of 13 with Command of Animals, and then works out with the GMs exactly how her animal empathy works. Later, as Maylene progresses, her power grows. She spends the 2xp on Extra Magic Ability to add another ability to her Command of Animals skill. Now, she can also use a charm/suggestion effect on animals to get them to help her. Whether she is attempted to read the animal's emotions, or whether she is attempting to charm them, she rolls with her Command of Animals skill, which has a skill level of 13. Maylene can spend xp on Command of Animals to increase her skill level, and it would apply to both abilities. She could also spend xp on Natural Aid to make animals stronger, and then Shapeshifting to turn into an animal herself.
Magic giving a bonus to Skills
If you would like to make up a magical ability that gives a bonus to a skill, here is a recommended mechanic: Choose a single skill when you describe your magical ability. When you roll with that magic skill, you add a bonus to that chosen skill equal to half your margin of success, round up, minimum 1.
Magic giving a bonus to Attributes
If you would like to make up a magical ability that gives a bonus to an attribute, here is a recommended mechanic: Choose a single attribute when you describe your magical ability. When you roll with that magic skill, you add a bonus to that attribute equal to your a quarter of your margin of success, round up, minimum 1.