TL;DR : Even though Angela's explanation made no sense to Eragon (or the reader), it's enough that she understands the connection between time, motion, heat, and energy.
What She Meant by Her Explanation
In the Inheritance Cycle universe, magic is simply an understanding of things. Once you understand a thing, you can control a thing.
In the movie Eragon, Brom explains magic to young Eragon like this:
BROM: Magic must be your last resort. It has rules. It has
limitations. And before you cast a spell, you must first learn the
ancient language of the elves.
BROM: Brisingr means "fire," it is fire. The thing is the word. Know
the word, and you can control the thing.
In the books, Eragon later learns that even the word isn't necessary - it's the thought behind the word that matters. Master spellcasters can perform magic without any spoken word or visible gesture. And, as Brom explains in the book, it doesn't matter whether or not there is an obvious connection between the thought and the object being affected, as long as the connection is solid within the caster's mind.
So, long story short, and there's a bit of hand-waving involved here, but essentially understanding the connection between things allows a caster to affect those things when casting a spell... even when the connection doesn't make sense to anyone else.
As to WHAT she actually did to the men, the book is unclear. Here is the scene in question:
He had only covered a few feet, however, when a flicker of movement
appeared next to each man: a soft, shadowy blur, like the motion of a
windblown pennant seen at the edge of his vision.
Without so much as a single cry, the twenty men stiffened and fell to
the floor, dead, every last one of them.
Alarmed, Eragon slowed to a stop before he ran into the bodies. Each
of the men had been stabbed through an eye, as neat as could be.
Speculation on the "How" part
Without further explanation or description, and given Angela's answer as to how she killed them, my personal speculation is that she stabbed each man through the eye with what was essentially a dagger made of super-heated air.
The "blur", described as a motion seen out of the corner of your eye, reminds me of the heat wave you see above intense heat. And even though Angela is known for answering questions with nonsense, she does specifically say that heat & energy are the same thing. And when you heat up air enough, you get plasma. TLDR, she knifed each one with a miniature invisible lightsaber right through the eye.