The Laundry RPG book says that when you pass 50% or 75% in one of a set of particular skills you get a check to learn sorcery skill, but I can't find anywhere that it says what value it starts at if you pass the check. One of my players is playing a Type III Deep One hybrid, which per the description in the Agent's Handbook get a check to learn sorcery when their Call of the Deep taint reaches those thresholds.
I'm going to answer from knowledge of BRP (4th edition/Call of Cthulhu) not the Laundry RPG, which I haven't played, so take this answer with a big ol' grain of salt.
In general, in BRP, you get skill advancement checks when you succeed in a skill check that advances the scenario. In 6th edition Call of Cthulhu, at the end of the scenario, you roll each skill that got a check during the scenario. If the roll rolls over the current level of the skill, you add +1d10 points to the skill.
Judging from what you've said, I'd read it as you get a skill check for sorcery. At the end of the scenario (or whenever The Laundry says you do advancement), you'd roll your sorcery. Since it starts at 00% (check the base value on the character sheet), should be no need to roll, you couldn't possibly roll under 00%. Then, add +1d10 to the skill (or whatever die The Laundry normally uses to improve skills).