The way they're described has me a little stumped as well. The beginning of the book makes them look like the Mage's Arts, meaning you'd have to undergo Initiation into one of the Ways. Initiation isn't allowed during CharGen, and most GMs are hesitant to house rule allowing it. So that would mean you have to wait for gameplay, and pay for it the same you would any other Initiation. But at that point, it's not a Quality or a Martial Art, it's just a thing you do (like the Mage Arts).
But later the book sells you Ways as 20 point Qualities. And I'm not seeing anything in there that would disallow purchasing them at CharGen. In fact, purchasing them post-CharGen would cost 40 points, which is far more than Initiations usually run.
So... I really wonder how they meant for Ways to be purchased. However, if you're using the Quality route, then yes it should be among your Qualities (which means you only have 5 left). Perhaps a reason to wait and buy the Way later through a 13 point Initiation instead?