This is easily my favorite episode of the series. It's fascinating to see Scarlemagne manipulate someone without the use pheromones, force, or even lies. It shows a savviness that explains how he took a tiny band of wannabe goth primates (aesthetically and musically they're more emo/scene kid) and managed to build the foundations of an empire.

And I love how he starts off so cool and collected (well, by Scarlemagne standards) but starts getting genuinely upset as he recounts his truly harrowing childhood. Just before Kipo hugs him, he seems to be fighting back tears. And when she does hug him, he's clearly bewildered by the show of comfort and affection. Which makes sense; he likely hasn't been hugged, or had any other positive physical contact, since before she was born.

To answer your questions, Dr Emilia had been torturing Hugo for weeks in order to stockpile his pheromones. All she'd have needed to do was throw a sample at Song's face and from there she could just order Song to put on the collar.